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Affiliation(s)
| | - C J F Spry
- St George's Hospital Medical School, London SW17
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Caballero OL, Shousha S, Zhao Q, Simpson AJG, Coombes RC, Neville AM. Expression of Cancer/Testis genes in ductal carcinoma in situ and benign lesions of the breast. Oncoscience 2013; 1:14-20. [PMID: 25593980 PMCID: PMC4295763 DOI: 10.18632/oncoscience.4] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2013] [Accepted: 12/10/2013] [Indexed: 01/22/2023] Open
Abstract
Cancer/testis (CT) genes represent a unique class of genes, which are expressed by germ cells, normally silenced in somatic cells, but activated in various cancers. CT proteins can elicit spontaneous immune responses in cancer patients and this feature makes them attractive targets for immunotherapy-based approaches. We have previously reported that CTs are relatively commonly expressed in estrogen receptor (ER) negative, high risk carcinomas. In this study, we examined the expression of selected CT genes in ductal carcinoma in situ (DCIS), lobular carcinoma in situ (LCIS) and benign proliferative lesions of the breast. ER negative DCIS were found to be associated with significant CT gene expression together with HER2 positivity and a marked stromal immune response.
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Affiliation(s)
- Otavia L Caballero
- Ludwig Collaborative Laboratory, Ludwig Institute for Cancer Research, Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Sami Shousha
- Imperial College Healthcare NHS Trust & Imperial College, London, Charing Cross Hospital
| | - Qi Zhao
- Ludwig Collaborative Laboratory, Ludwig Institute for Cancer Research, Department of Neurosurgery, The Johns Hopkins University School of Medicine, Baltimore, MD USA
| | - Andrew J G Simpson
- Ludwig Institute for Cancer Research, New York, NY., USA.,Current affiliation: Orygen Biotecnologia, São Paulo, Brazil
| | - R Charles Coombes
- Imperial College Healthcare NHS Trust & Imperial College, London, Charing Cross Hospital
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Pagotto A, Caballero OL, Volkmar N, Devalle S, Simpson AJG, Lu X, Christianson JC. Centrosomal localisation of the cancer/testis (CT) antigens NY-ESO-1 and MAGE-C1 is regulated by proteasome activity in tumour cells. PLoS One 2013; 8:e83212. [PMID: 24340093 PMCID: PMC3858345 DOI: 10.1371/journal.pone.0083212] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/31/2013] [Indexed: 02/03/2023] Open
Abstract
The Cancer/Testis (CT) antigen family of genes are transcriptionally repressed in most human tissues but are atypically re-expressed in many malignant tumour types. Their restricted expression profile makes CT antigens ideal targets for cancer immunotherapy. As little is known about whether CT antigens may be regulated by post-translational processing, we investigated the mechanisms governing degradation of NY-ESO-1 and MAGE-C1 in selected cancer cell lines. Inhibitors of proteasome-mediated degradation induced the partitioning of NY-ESO-1 and MAGE-C1 into a detergent insoluble fraction. Moreover, this treatment also resulted in increased localisation of NY-ESO-1 and MAGE-C1 at the centrosome. Despite their interaction, relocation of either NY-ESO-1 or MAGE-C1 to the centrosome could occur independently of each other. Using a series of truncated fragments, the regions corresponding to NY-ESO-191-150 and MAGE-C1900-1116 were established as important for controlling both stability and localisation of these CT antigens. Our findings demonstrate that the steady state levels of NY-ESO-1 and MAGE-C1 are regulated by proteasomal degradation and that both behave as aggregation-prone proteins upon accumulation. With proteasome inhibitors being increasingly used as front-line treatment in cancer, these data raise issues about CT antigen processing for antigenic presentation and therefore immunogenicity in cancer patients.
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Affiliation(s)
- Anna Pagotto
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, United Kingdom
| | - Otavia L. Caballero
- Ludwig Collaborative Group, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Norbert Volkmar
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, United Kingdom
| | - Sylvie Devalle
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan-Kettering Cancer Center, New York, New York, United States of America
| | - Andrew J. G. Simpson
- Ludwig Collaborative Group, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America
| | - Xin Lu
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, United Kingdom
- * E-mail:
| | - John C. Christianson
- Ludwig Institute for Cancer Research, Nuffield Department of Clinical Medicine, University of Oxford, Headington, Oxford, United Kingdom
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5
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Abstract
Cancer/testis (CT) genes are encoded by genes that are normally expressed only in the human germ line but which are activated in various malignancies. CT proteins are frequently immunogenic in cancer patients and their expression is highly restricted to tumors. They are thus important targets for anticancer immunotherapy. In several different tumor types, the expression of CT-X genes is associated with advanced disease and poor outcome, indicating that their expression might contribute to tumorigenesis. CT-X genes encoding members of the MAGE protein family on Xq28 have been shown to potentially influence the tumorigenic phenotype. We used small interfering RNA (siRNA) to investigate whether CT-X mapping to the short arm of the X-chromosome might also have tumorigenic properties and therefore be potentially targeted by functional inhibitors in a therapeutic setting. siRNAs specific to GAGE, SSX and XAGE1 were used in cell proliferation, migration and cell survival assays using cell lines derived from melanoma, a tumor type known to present high frequencies of expression of CT antigens. We found that of these, those specific to GAGE and XAGE1 most significantly impeded melanoma cell migration and invasion and those specific to SSX4 and XAGE1 decreased the clonogenic survival of melanoma cells. Our results suggest that GAGE, XAGE1 and SSX4 might each have a role in tumor progression and are possible therapeutic targets for the treatment of melanoma and other malignancies.
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Affiliation(s)
- Otavia L Caballero
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan-Kettering Cancer Center, New York, USA.
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Baia GS, Caballero OL, Ho JSY, Zhao Q, Cohen T, Binder ZA, Salmasi V, Gallia GL, Quinones-Hinojosa A, Olivi A, Brem H, Burger P, Strausberg RL, Simpson AJG, Eberhart CG, Riggins GJ. NY-ESO-1 expression in meningioma suggests a rationale for new immunotherapeutic approaches. Cancer Immunol Res 2013; 1:296-302. [PMID: 24777967 DOI: 10.1158/2326-6066.cir-13-0029] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [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: 11/16/2022]
Abstract
Meningiomas are the most common primary intracranial tumors. Surgical resection remains the treatment of choice for these tumors. However, a significant number of tumors are not surgically accessible, recur, or become malignant, necessitating the repetition of surgery and sometimes radiation. Chemotherapy is rarely used and is generally not recognized as an effective treatment. Cancer/testis (CT) genes represent a unique class of genes, which are expressed by germ cells, normally silenced in somatic cells, but activated in various cancers. CT proteins can elicit spontaneous immune responses in patients with cancer and this feature makes them attractive targets for immunotherapy-based approaches. We analyzed mRNA expression of 37 testis-restricted CT genes in a discovery set of 18 meningiomas by reverse transcription PCR. The overall frequency of expression of CT genes ranged from 5.6% to 27.8%. The most frequently expressed was NY-ESO-1, in 5 patients (27.8%). We subsequently analyzed NY-ESO-1 protein expression in a larger set of meningiomas by immunohistochemistry and found expression in 108 of 110 cases. In some cases, NY-ESO-1 expression was diffused and homogenous, but in most instances it was heterogeneous. Importantly, NY-ESO-1 expression was positively correlated with higher grade and patients presenting with higher levels of NY-ESO-1 staining had significantly worse disease-free and overall survival. We have also shown that NY-ESO-1 expression may lead to humoral immune response in patients with meningioma. Considering the limited treatment options for patients with meningioma, the potential of NY-ESO-1-based immunotherapy should be explored.
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Affiliation(s)
- Gilson S Baia
- Authors' Affiliations: New York Branch at Memorial Sloan-Kettering Cancer Center, New York, New York
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7
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Zhao Q, Caballero OL, Simpson AJG, Strausberg RL. Differential evolution of MAGE genes based on expression pattern and selection pressure. PLoS One 2012; 7:e48240. [PMID: 23133577 PMCID: PMC3484994 DOI: 10.1371/journal.pone.0048240] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [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: 02/15/2012] [Accepted: 09/28/2012] [Indexed: 11/18/2022] Open
Abstract
Starting from publicly-accessible datasets, we have utilized comparative and phylogenetic genome analyses to characterize the evolution of the human MAGE gene family. Our characterization of genomic structures in representative genomes of primates, rodents, carnivora, and macroscelidea indicates that both Type I and Type II MAGE genes have undergone lineage-specific evolution. The restricted expression pattern in germ cells of Type I MAGE orthologs is observed throughout evolutionary history. Unlike Type II MAGEs that have conserved promoter sequences, Type I MAGEs lack promoter conservation, suggesting that epigenetic regulation is a central mechanism for controlling their expression. Codon analysis shows that Type I but not Type II MAGE genes have been under positive selection. The combination of genomic and expression analysis suggests that Type 1 MAGE promoters and genes continue to evolve in the hominin lineage, perhaps towards functional diversification or acquiring additional specific functions, and that selection pressure at codon level is associated with expression spectrum.
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Affiliation(s)
- Qi Zhao
- Ludwig Collaborative Laboratory, Department of Neurosurgery, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.
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Ma Y, Kowolik CM, Swiderski PM, Kortylewski M, Yu H, Horne DA, Jove R, Caballero OL, Simpson AJG, Lee FT, Pillay V, Scott AM. Humanized Lewis-Y specific antibody based delivery of STAT3 siRNA. ACS Chem Biol 2011; 6:962-70. [PMID: 21766840 DOI: 10.1021/cb200176v] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The clinical application of siRNA is limited largely by the lack of efficient, cell-specific delivery systems. Antibodies are attractive delivery vehicles for targeted therapy due to their high specificity. In this study we describe the use of a humanized monoclonal antibody (mAb), hu3S193, against Lewis-Y (Le(y)), as a delivery vehicle for STAT3 siRNA. This mAb is rapidly internalized into Le(y)-expressing cancer cells via antigen recognition, and when coupled to STAT3 siRNA, a potentially powerful molecularly targeted delivery agent is created. Selective silencing of STAT3 is associated with tumor suppression. Two hu3S193 based siRNA delivery systems using STAT3 siRNA as a prototype were developed and tested in Le(y)-positive cancer cells: (a) a covalent construct based on a reductive disulfide linker that is expected to undergo cleavage within cells and (b) a noncovalent construct based on (d-arginine)(9) (9r) modified hu3S193. Le(y)-specific binding and internalization of both the covalent and noncovalent constructs were confirmed by flow cytometry and confocal microscopy. Both the covalent and the noncovalent system led to efficient STAT3 silencing in Le(y)-positive cancer cells (A431) but not in Le(y)-negative cancer cells (MDA-MB-435). The covalent construct, however, required co-treatment with reagents such as chloroquine or 9r that facilitate the escape of the siRNA from endosomes to achieve significant gene silencing. The 9r modified noncovalent construct induced ∼70% STAT3 knockdown at submicromolar siRNA concentrations when used at an optimal vehicle-to-siRNA ratio of 5:1. The STAT3 knockdown also led to ∼50% inhibition of cell proliferation of Le(y)-positive cells. Noncovalent linked STAT3 siRNA-hu3S193 has great promise for targeted knockdown of STAT3 in tumor cells.
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Affiliation(s)
| | | | | | | | | | | | | | - Otavia L. Caballero
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan-Kettering Cancer Center, New York, New York 10021, United States
| | - Andrew J. G. Simpson
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan-Kettering Cancer Center, New York, New York 10021, United States
| | - Fook-Thean Lee
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Austin Hospital, Heidelberg, VIC, 3084, Australia
| | - Vinochani Pillay
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Austin Hospital, Heidelberg, VIC, 3084, Australia
| | - Andrew M. Scott
- Ludwig Institute for Cancer Research, Melbourne-Austin Branch, Austin Hospital, Heidelberg, VIC, 3084, Australia
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Galante PAF, Parmigiani RB, Zhao Q, Caballero OL, de Souza JE, Navarro FCP, Gerber AL, Nicolás MF, Salim ACM, Silva APM, Edsall L, Devalle S, Almeida LG, Ye Z, Kuan S, Pinheiro DG, Tojal I, Pedigoni RG, de Sousa RGMA, Oliveira TYK, de Paula MG, Ohno-Machado L, Kirkness EF, Levy S, da Silva WA, Vasconcelos ATR, Ren B, Zago MA, Strausberg RL, Simpson AJG, de Souza SJ, Camargo AA. Distinct patterns of somatic alterations in a lymphoblastoid and a tumor genome derived from the same individual. Nucleic Acids Res 2011; 39:6056-68. [PMID: 21493686 PMCID: PMC3152357 DOI: 10.1093/nar/gkr221] [Citation(s) in RCA: 18] [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] [Indexed: 11/12/2022] Open
Abstract
Although patterns of somatic alterations have been reported for tumor genomes, little is known on how they compare with alterations present in non-tumor genomes. A comparison of the two would be crucial to better characterize the genetic alterations driving tumorigenesis. We sequenced the genomes of a lymphoblastoid (HCC1954BL) and a breast tumor (HCC1954) cell line derived from the same patient and compared the somatic alterations present in both. The lymphoblastoid genome presents a comparable number and similar spectrum of nucleotide substitutions to that found in the tumor genome. However, a significant difference in the ratio of non-synonymous to synonymous substitutions was observed between both genomes (P = 0.031). Protein-protein interaction analysis revealed that mutations in the tumor genome preferentially affect hub-genes (P = 0.0017) and are co-selected to present synergistic functions (P < 0.0001). KEGG analysis showed that in the tumor genome most mutated genes were organized into signaling pathways related to tumorigenesis. No such organization or synergy was observed in the lymphoblastoid genome. Our results indicate that endogenous mutagens and replication errors can generate the overall number of mutations required to drive tumorigenesis and that it is the combination rather than the frequency of mutations that is crucial to complete tumorigenic transformation.
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Affiliation(s)
- Pedro A F Galante
- Ludwig Institute for Cancer Research, São Paulo Branch at Hospital Alemão Oswaldo Cruz, São Paulo 01323-903, Brazil
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10
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Valsesia A, Rimoldi D, Martinet D, Ibberson M, Benaglio P, Quadroni M, Waridel P, Gaillard M, Pidoux M, Rapin B, Rivolta C, Xenarios I, Simpson AJG, Antonarakis SE, Beckmann JS, Jongeneel CV, Iseli C, Stevenson BJ. Network-guided analysis of genes with altered somatic copy number and gene expression reveals pathways commonly perturbed in metastatic melanoma. PLoS One 2011; 6:e18369. [PMID: 21494657 PMCID: PMC3072964 DOI: 10.1371/journal.pone.0018369] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2010] [Accepted: 02/28/2011] [Indexed: 12/21/2022] Open
Abstract
Cancer genomes frequently contain somatic copy number alterations (SCNA) that can significantly perturb the expression level of affected genes and thus disrupt pathways controlling normal growth. In melanoma, many studies have focussed on the copy number and gene expression levels of the BRAF, PTEN and MITF genes, but little has been done to identify new genes using these parameters at the genome-wide scale. Using karyotyping, SNP and CGH arrays, and RNA-seq, we have identified SCNA affecting gene expression ('SCNA-genes') in seven human metastatic melanoma cell lines. We showed that the combination of these techniques is useful to identify candidate genes potentially involved in tumorigenesis. Since few of these alterations were recurrent across our samples, we used a protein network-guided approach to determine whether any pathways were enriched in SCNA-genes in one or more samples. From this unbiased genome-wide analysis, we identified 28 significantly enriched pathway modules. Comparison with two large, independent melanoma SCNA datasets showed less than 10% overlap at the individual gene level, but network-guided analysis revealed 66% shared pathways, including all but three of the pathways identified in our data. Frequently altered pathways included WNT, cadherin signalling, angiogenesis and melanogenesis. Additionally, our results emphasize the potential of the EPHA3 and FRS2 gene products, involved in angiogenesis and migration, as possible therapeutic targets in melanoma. Our study demonstrates the utility of network-guided approaches, for both large and small datasets, to identify pathways recurrently perturbed in cancer.
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Affiliation(s)
- Armand Valsesia
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Donata Rimoldi
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
| | - Danielle Martinet
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Mark Ibberson
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | - Paola Benaglio
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | - Manfredo Quadroni
- Protein Analysis Facility, Center for Integrative Genomics, Lausanne, Switzerland
| | - Patrice Waridel
- Protein Analysis Facility, Center for Integrative Genomics, Lausanne, Switzerland
| | - Muriel Gaillard
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Mireille Pidoux
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Blandine Rapin
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - Carlo Rivolta
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
| | | | - Andrew J. G. Simpson
- Ludwig Institute for Cancer Research, New York, New York, United States of America
| | | | - Jacques S. Beckmann
- Department of Medical Genetics, University of Lausanne, Lausanne, Switzerland
- Service of Medical Genetics, Centre Hospitalier Universitaire Vaudois, Lausanne, Switzerland
| | - C. Victor Jongeneel
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- Institute for Genomic Biology and National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Champaign, Illinois, United States of America
| | - Christian Iseli
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail: (CI); (BJS)
| | - Brian J. Stevenson
- Ludwig Institute for Cancer Research, Lausanne, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
- * E-mail: (CI); (BJS)
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Röhrig UF, Awad L, Grosdidier A, Larrieu P, Stroobant V, Colau D, Cerundolo V, Simpson AJG, Vogel P, Van den Eynde BJ, Zoete V, Michielin O. Rational design of indoleamine 2,3-dioxygenase inhibitors. J Med Chem 2010; 53:1172-89. [PMID: 20055453 DOI: 10.1021/jm9014718] [Citation(s) in RCA: 128] [Impact Index Per Article: 9.1] [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: 01/10/2023]
Abstract
Indoleamine 2,3-dioxygenase (IDO) is an important therapeutic target for the treatment of diseases such as cancer that involve pathological immune escape. We have used the evolutionary docking algorithm EADock to design new inhibitors of this enzyme. First, we investigated the modes of binding of all known IDO inhibitors. On the basis of the observed docked conformations, we developed a pharmacophore model, which was then used to devise new compounds to be tested for IDO inhibition. We also used a fragment-based approach to design and to optimize small organic molecule inhibitors. Both approaches yielded several new low-molecular weight inhibitor scaffolds, the most active being of nanomolar potency in an enzymatic assay. Cellular assays confirmed the potential biological relevance of four different scaffolds.
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Affiliation(s)
- Ute F Röhrig
- Ludwig Institute for Cancer Research, Lausanne Branch, CH-1015 Lausanne, Switzerland
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12
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Bettoni F, Filho FC, Grosso DM, Galante PAF, Parmigiani RB, Geraldo MV, Henrique-Silva F, Oba-Shinjo SM, Marie SKN, Soares FA, Brentani HP, Simpson AJG, de Souza SJ, Camargo AA. Identification of FAM46D as a novel cancer/testis antigen using EST data and serological analysis. Genomics 2009; 94:153-60. [PMID: 19540335 DOI: 10.1016/j.ygeno.2009.06.001] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 05/13/2009] [Accepted: 06/11/2009] [Indexed: 11/28/2022]
Abstract
Cancer/testis Antigens (CTAs) are immunogenic proteins with a restricted expression pattern in normal tissues and aberrant expression in different types of tumors being considered promising candidates for immunotherapy. We used the alignment between EST sequences and the human genome sequence to identify novel CT genes. By examining the EST tissue composition of known CT clusters we defined parameters for the selection of 1184 EST clusters corresponding to putative CT genes. The expression pattern of 70 CT gene candidates was evaluated by RT-PCR in 21 normal tissues, 17 tumor cell lines and 160 primary tumors. We were able to identify 4 CT genes expressed in different types of tumors. The presence of antibodies against the protein encoded by 1 of these 4 CT genes (FAM46D) was exclusively detected in plasma samples from cancer patients. Due to its restricted expression pattern and immunogenicity FAM46D represents a novel target for cancer immunotherapy.
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Affiliation(s)
- Fabiana Bettoni
- Ludwig Institute for Cancer Research, Hospital Alemão Oswaldo Cruz, São Paulo, SP, Brazil
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13
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Tendler M, Simpson AJG. The biotechnology-value chain: development of Sm14 as a schistosomiasis vaccine. Acta Trop 2008; 108:263-6. [PMID: 18834847 DOI: 10.1016/j.actatropica.2008.09.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2007] [Revised: 07/18/2008] [Accepted: 09/01/2008] [Indexed: 11/28/2022]
Abstract
In the 1990s, WHO/TDR created a product development program and initiated collaborations with other major international donors to promote rapid vaccine development and other tools for the control of endemic diseases. This "push strategy" was chosen to achieve effective research projects fostering innovation in the context of rapid product development. In the field of vaccine development, the aim was to bring forth ways and means to immunize against the most important human parasite diseases. Although the malaria vaccine projects scored initial successes it has been difficult to move forward decidedly. With regard to schistosomiasis, more than 10 important antigens with strong potential as vaccines candidates emerged from the several 100 scientific projects supported by international donor agencies and national research programs over the last few decades. Among those still seriously pursued, the Fatty Acid-Binding Protein (FABP)-14 kDa Schistosoma mansoni (Sm14) antigen stands out, both due to its steady progress towards field trials and because it represents the sole vaccine candidate to emerge from an endemic country. Work has now progressed to the scale-up level and an industrial production process has successfully been put in place. The very special feature of Sm14 is its strong immunological reactivity with an antigen shared between two different important parasites, which give this vaccine candidate the potential to be used against more than one infection. It has been demonstrated that it has effect not only against S. mansoni in humans but also against Fasciola hepatica, a parasite that causes disease in cattle and sheep leading to annual losses over 3 $US billion to the food industry worldwide. The Sm14 patents, granted to Oswaldo Cruz Foundation (FIOCRUZ), a Brazilian scientific institution directly linked to the Brazilian Ministry of Health, have been licensed to a private company which has the intention to lead the Sm14 project to success, both in the veterinary and in the human field. The objective is to provide economic performance by fostering scientific and economic progress and thus reach the global market. Sm14 is at present at the stage of planning clinical trials under a private-public partnership (PPP) initiative in collaboration with FIOCRUZ which has recently received significant financial support from FINEP, a public Brazilian Financial Agency.
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Affiliation(s)
- Miriam Tendler
- Fundação Oswaldo Cruz, Laboratório de Esquistossomose Experimental, Av. Brasil, 4365, Manguinhos, Rio de Janeiro, RJ, CEP: 21-045-900, Brazil Institute FIOCRUZ, Brazil.
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14
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Almeida LG, Sakabe NJ, deOliveira AR, Silva MCC, Mundstein AS, Cohen T, Chen YT, Chua R, Gurung S, Gnjatic S, Jungbluth AA, Caballero OL, Bairoch A, Kiesler E, White SL, Simpson AJG, Old LJ, Camargo AA, Vasconcelos ATR. CTdatabase: a knowledge-base of high-throughput and curated data on cancer-testis antigens. Nucleic Acids Res 2008; 37:D816-9. [PMID: 18838390 PMCID: PMC2686577 DOI: 10.1093/nar/gkn673] [Citation(s) in RCA: 294] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
The potency of the immune response has still to be harnessed effectively to combat human cancers. However, the discovery of T-cell targets in melanomas and other tumors has raised the possibility that cancer vaccines can be used to induce a therapeutically effective immune response against cancer. The targets, cancer-testis (CT) antigens, are immunogenic proteins preferentially expressed in normal gametogenic tissues and different histological types of tumors. Therapeutic cancer vaccines directed against CT antigens are currently in late-stage clinical trials testing whether they can delay or prevent recurrence of lung cancer and melanoma following surgical removal of primary tumors. CT antigens constitute a large, but ill-defined, family of proteins that exhibit a remarkably restricted expression. Currently, there is a considerable amount of information about these proteins, but the data are scattered through the literature and in several bioinformatic databases. The database presented here, CTdatabase (http://www.cta.lncc.br), unifies this knowledge to facilitate both the mining of the existing deluge of data, and the identification of proteins alleged to be CT antigens, but that do not have their characteristic restricted expression pattern. CTdatabase is more than a repository of CT antigen data, since all the available information was carefully curated and annotated with most data being specifically processed for CT antigens and stored locally. Starting from a compilation of known CT antigens, CTdatabase provides basic information including gene names and aliases, RefSeq accession numbers, genomic location, known splicing variants, gene duplications and additional family members. Gene expression at the mRNA level in normal and tumor tissues has been collated from publicly available data obtained by several different technologies. Manually curated data related to mRNA and protein expression, and antigen-specific immune responses in cancer patients are also available, together with links to PubMed for relevant CT antigen articles.
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Oba-Shinjo SM, Caballero OL, Jungbluth AA, Rosemberg S, Old LJ, Simpson AJG, Marie SKN. Cancer-testis (CT) antigen expression in medulloblastoma. Cancer Immun 2008; 8:7. [PMID: 18426187 PMCID: PMC2935780] [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] [Subscribe] [Scholar Register] [Received: 08/16/2007] [Revised: 02/06/2008] [Accepted: 03/07/2008] [Indexed: 05/26/2023]
Abstract
Medulloblastoma is the most common childhood malignant tumor of the central nervous system. Treatment of medulloblastoma requires harmful therapy and nevertheless carries a poor prognosis. Due to their presence in various cancers and their limited expression in normal tissues, CT antigens are ideal vaccine targets for tumor immunotherapy. CT antigens, such as MAGE and NY-ESO-1, have been employed in clinical trials in various malignancies but little is known about their presence in medulloblastoma. We analyzed 25 medulloblastomas for the expression of a panel of CT antigens by RT-PCR and immunohistochemistry. Messenger RNA expression in the samples was as follows: GAGE 64%, MAGEA3/6 56%, SYCP1 44%, SLCO6A1 32%, MAGEC1 28%, MAGEC2 28%, MAGEA4 28%, NY-ESO-1 20%, MAGEA1 16%, and TPTE 0%. All cases except one (96%) were positive for mRNA expression of at least one CT gene. However, CT antigen expression was scarce on a protein level. Immunoreaction to monoclonal antibody E978 (NY-ESO-1) was negative in all cases; MA454 (MAGEA1), 57B (MAGEA4), M3H67 (MAGEA3/6), CT10#5 (MAGEC2) and #23 (GAGE) were each positive in 1 case, while the highest incidence of positive immunostaining, albeit heterogeneous, was seen with CT7-33 (MAGEC1) in 3 out of the 25 cases. The absence of correlation between mRNA and protein expression in medulloblastoma has not been observed in other tumors and further studies addressing the biology of CT antigens are necessary to investigate the present discrepant results.
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Affiliation(s)
- Sueli M Oba-Shinjo
- Department of Neurology, School of Medicine, University of São Paulo, Av Dr Arnaldo, 455, room 4110, São Paulo, Brazil
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16
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Yang B, O'Herrin SM, Wu J, Reagan-Shaw S, Ma Y, Bhat KMR, Gravekamp C, Setaluri V, Peters N, Hoffmann FM, Peng H, Ivanov AV, Simpson AJG, Longley BJ. MAGE-A, mMage-b, and MAGE-C proteins form complexes with KAP1 and suppress p53-dependent apoptosis in MAGE-positive cell lines. Cancer Res 2007; 67:9954-62. [PMID: 17942928 DOI: 10.1158/0008-5472.can-07-1478] [Citation(s) in RCA: 213] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The MAGE-A, MAGE-B, and MAGE-C protein families comprise the class-I MAGE/cancer testes antigens, a group of highly homologous proteins whose expression is suppressed in all normal tissues except developing sperm. Aberrant expression of class I MAGE proteins occurs in melanomas and many other malignancies, and MAGE proteins have long been recognized as tumor-specific targets; however, their functions have largely been unknown. Here, we show that suppression of class I MAGE proteins induces apoptosis in the Hs-294T, A375, and S91 MAGE-positive melanoma cell lines and that members of all three families of MAGE class I proteins form complexes with KAP1, a scaffolding protein that is known as a corepressor of p53 expression and function. In addition to inducing apoptosis, MAGE suppression decreases KAP1 complexing with p53, increases immunoreactive and acetylated p53, and activates a p53 responsive reporter gene. Suppression of class I MAGE proteins also induces apoptosis in MAGE-A-positive, p53wt/wt parental HCT 116 colon cancer cells but not in a MAGE-A-positive HCT 116 p53-/- variant, indicating that MAGE suppression of apoptosis requires p53. Finally, treatment with MAGE-specific small interfering RNA suppresses S91 melanoma growth in vivo, in syngenic DBA2 mice. Thus, class I MAGE protein expression may suppress apoptosis by suppressing p53 and may actively contribute to the development of malignancies and by promoting tumor survival. Because the expression of class I MAGE proteins is limited in normal tissues, inhibition of MAGE antigen expression or function represents a novel and specific treatment for melanoma and diverse malignancies.
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Affiliation(s)
- Bing Yang
- Department of Dermatology and Paul P. Carbone Comprehensive Cancer Center, University of Wisconsin Medical School, Madison, Wisconsin 53706, USA.
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17
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Silva WA, Gnjatic S, Ritter E, Chua R, Cohen T, Hsu M, Jungbluth AA, Altorki NK, Chen YT, Old LJ, Simpson AJG, Caballero OL. PLAC1, a trophoblast-specific cell surface protein, is expressed in a range of human tumors and elicits spontaneous antibody responses. Cancer Immun 2007; 7:18. [PMID: 17983203 PMCID: PMC2935750] [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] [Subscribe] [Scholar Register] [Received: 10/04/2007] [Accepted: 10/31/2007] [Indexed: 05/25/2023]
Abstract
Identification of genes that are upregulated in tumors, and whose normal expression excludes adult somatic tissues but includes germline and/or embryonic tissues, has resulted in a rich variety of cancer antigens that are attractive targets for cancer vaccine and other therapeutic approaches. In the present study, we extended this approach to include genes strongly and restrictively expressed in the placenta by mining publicly available SAGE and EST databases. We identified a number of genes with high expression in placenta and different cancer types but with relatively restricted expression in normal tissues. The gene with the most distinctive expression pattern was found to be PLAC1, which encodes a putative cell surface protein that is highly expressed in placenta, testis, cancer cell lines and lung tumors. Hence we have designated it CT92. We found by ELISA that PLAC1 is immunogenic in a subset of cancer patients and healthy women. Its physical and expression characteristics render it a potential target for both active and passive cancer immunotherapeutic strategies.
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Affiliation(s)
- Wilson A. Silva
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
- Department of Genetics, Faculty of Medicine
of Ribeirão Preto, São Paulo UniversityRibeirão
PretoSão PauloBrazil
| | - Sacha Gnjatic
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
| | - Erika Ritter
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
| | - Ramon Chua
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
| | - Tzeela Cohen
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
| | - Melinda Hsu
- Weill Medical College1300
York AvenueNew York, NYUSA
| | - Achim A. Jungbluth
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
| | | | | | - Lloyd J. Old
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
| | - Andrew J. G. Simpson
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
| | - Otavia L. Caballero
- Ludwig Institute for Cancer Research,
New York Branch at Memorial Sloan-Kettering Cancer CenterNew
York, NYUSA
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18
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Spisek R, Kukreja A, Chen LC, Matthews P, Mazumder A, Vesole D, Jagannath S, Zebroski HA, Simpson AJG, Ritter G, Durie B, Crowley J, Shaughnessy JD, Scanlan MJ, Gure AO, Barlogie B, Dhodapkar MV. Frequent and specific immunity to the embryonal stem cell-associated antigen SOX2 in patients with monoclonal gammopathy. ACTA ACUST UNITED AC 2007; 204:831-40. [PMID: 17389240 PMCID: PMC2118551 DOI: 10.1084/jem.20062387] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Specific targets of cellular immunity in human premalignancy are largely unknown. Monoclonal gammopathy of undetermined significance (MGUS) represents a precursor lesion to myeloma (MM). We show that antigenic targets of spontaneous immunity in MGUS differ from MM. MGUS patients frequently mount a humoral and cellular immune response against SOX2, a gene critical for self-renewal in embryonal stem cells. Intranuclear expression of SOX2 marks the clonogenic CD138− compartment in MGUS. SOX2 expression is also detected in a proportion of CD138+ cells in MM patients. However, these patients lack anti-SOX2 immunity. Cellular immunity to SOX2 inhibits the clonogenic growth of MGUS cells in vitro. Detection of anti-SOX2 T cells predicts favorable clinical outcome in patients with asymptomatic plasmaproliferative disorders. Harnessing immunity to antigens expressed by tumor progenitor cells may be critical for prevention and therapy of human cancer.
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Affiliation(s)
- Radek Spisek
- Laboratory of Tumor Immunology and Immunotherapy, The Rockefeller University, New York, NY 10021, USA
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19
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Gallia GL, Rand V, Siu IM, Eberhart CG, James CD, Marie SKN, Oba-Shinjo SM, Carlotti CG, Caballero OL, Simpson AJG, Brock MV, Massion PP, Carson BS, Riggins GJ. PIK3CA gene mutations in pediatric and adult glioblastoma multiforme. Mol Cancer Res 2007; 4:709-14. [PMID: 17050665 DOI: 10.1158/1541-7786.mcr-06-0172] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.9] [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: 11/16/2022]
Abstract
The phosphatidylinositol 3-kinases (PI3K) are a family of enzymes that relay important cellular growth control signals. Recently, a large-scale mutational analysis of eight PI3K and eight PI3K-like genes revealed somatic mutations in PIK3CA, which encodes the p110alpha catalytic subunit of class IA PI3K, in several types of cancer, including glioblastoma multiforme. In that report, 4 of 15 (27%) glioblastomas contained potentially oncogenic PIK3CA mutations. Subsequent studies, however, showed a significantly lower mutation rate ranging from 0% to 7%. Given this disparity and to address the relation of patient age to mutation frequency, we examined 10 exons of PIK3CA in 73 glioblastoma samples by PCR amplification followed by direct DNA sequencing. Overall, PIK3CA mutations were found in 11 (15%) samples, including several novel mutations. PIK3CA mutations were distributed in all sample types, with 18%, 9%, and 13% of primary tumors, xenografts, and cell lines containing mutations, respectively. Of the primary tumors, PIK3CA mutations were identified in 21% and 17% of pediatric and adult samples, respectively. No evidence of PIK3CA gene amplification was detected by quantitative real-time PCR in any of the samples. This study confirms that PIK3CA mutations occur in a significant number of human glioblastomas, further indicating that therapeutic targeting of this pathway in glioblastomas is of value. Moreover, this is the first study showing PIK3CA mutations in pediatric glioblastomas, thus providing a molecular target in this important pediatric malignancy.
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Affiliation(s)
- Gary L Gallia
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 1550 Orleans Street, CRB II, Room 257, Baltimore, MD 21231, USA
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20
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Nelson PT, Zhang PJ, Spagnoli GC, Tomaszewski JE, Pasha TL, Frosina D, Caballero OL, Simpson AJG, Old LJ, Jungbluth AA. Cancer/testis (CT) antigens are expressed in fetal ovary. Cancer Immun 2007; 7:1. [PMID: 17217256 PMCID: PMC3077293] [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] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Accepted: 12/19/2006] [Indexed: 05/13/2023]
Abstract
Cancer/testis (CT) antigens are named after their expression pattern as they are typically present in various types of tumors and in the germ cells of normal adult testis. Adult ovarian tissue is usually reported to be CT antigen negative. Based on the differences in female versus male gonadal development, the ovarian counterpart of the most predominant CT antigen positive testicular germ cells are not prevalent in the adult ovary. Hence, we analyzed the protein expression of several CT antigens in fetal ovary by immunohistochemistry with various monoclonal antibodies (mAbs) previously generated by our group. The mAbs used were: MA454 (MAGE-A1), M3H67 (MAGE-A3), 57B (MAGE-A4), CT7-33 (CT7/MAGE-C1), and ES121 (NY-ESO-1). All mAbs showed some immunopositivity in fetal ovarian germ cells. The most intense staining was seen with mAbs M3H67, 57B, and CT7-33 during weeks 16-23 of gestation. The most prevalent cells stained were oogonia, with only focal staining of oocytes of the primordial follicle. We conclude that CT antigens are regularly expressed in fetal ovarian germ cells and might play an important role in male and female germ cell biology.
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Affiliation(s)
- Peter T Nelson
- Sanders-Brown Center on Aging and Dept of Pathology, University of Kentucky, Lexington, KY, USA
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21
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Cho HJ, Caballero OL, Gnjatic S, Andrade VCC, Colleoni GW, Vettore AL, Outtz HH, Fortunato S, Altorki N, Ferrera CA, Chua R, Jungbluth AA, Chen YT, Old LJ, Simpson AJG. Physical interaction of two cancer-testis antigens, MAGE-C1 (CT7) and NY-ESO-1 (CT6). Cancer Immun 2006; 6:12. [PMID: 17137291] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 09/26/2006] [Accepted: 10/10/2006] [Indexed: 05/12/2023]
Abstract
Cancer/testis (CT) antigens are the protein products of germ line-associated genes that are activated in a wide variety of tumors and can elicit autologous cellular and humoral immune responses. CT antigens can be divided between those that are encoded on the X chromosome (CT-X antigens) and those that are not (non-X CT antigens). Among the CT-X antigens, the melanoma antigen gene (MAGE) family, defined by a shared MAGE homology domain (MHD), is the largest. CT-X genes are frequently expressed in a coordinate manner in cancer cells, and their expression appears to be modulated by epigenetic mechanisms. The expression of CT-X genes is associated with advanced disease and poor outcome in different tumor types. We used the yeast two-hybrid system to identify putative MHD-interacting proteins. The MHD of MAGE-C1 (CT7) was used as bait to screen a human testis cDNA library. This study identified NY-ESO-1 (CT6) as a MAGE-C1 binding partner. Immunoprecipitation and immunofluorescence staining confirmed MAGE-C1 interaction with NY-ESO-1, and cytoplasmic co-localization of both proteins in melanoma cells. Co-expression of these two genes was found to occur in cancer cell lines from different origins, as well as in primary tumors (multiple myeloma and non-small cell lung cancer samples). This is the first report of direct interaction between two CT antigens and may be pertinent in the light of the frequently coordinated expression of these proteins.
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Affiliation(s)
- Hearn J Cho
- Weill Medical College of Cornell University, 1300 York Avenue, New York, NY 10021, USA
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22
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Parmigiani RB, Bettoni F, Vibranovski MD, Lopes MH, Martins WK, Cunha IW, Soares FA, Simpson AJG, de Souza SJ, Camargo AA. Characterization of a cancer/testis (CT) antigen gene family capable of eliciting humoral response in cancer patients. Proc Natl Acad Sci U S A 2006; 103:18066-71. [PMID: 17114284 PMCID: PMC1838707 DOI: 10.1073/pnas.0608853103] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2006] [Indexed: 01/03/2023] Open
Abstract
Cancer/testis (CT) antigens are immunogenic proteins expressed in normal gametogenic tissues and in different types of tumors. CT antigens are promising candidates for cancer immunotherapy, and the identification of novel CT antigens is a prerequisite for the development of cancer vaccines. We have identified a CT antigen, named CTSP-1, with partial similarity to the breast differentiation antigen NY-BR-1. CTSP-1 presents several splicing and polyadenylation variants and has a very restricted expression pattern among normal tissues. CTSP-1 is exclusively expressed in normal testis and is aberrantly expressed in 47.6% (10 of 21) of tumor cell lines and in 44.4% (75 of 169) of tumors from different histological types. The highest percentages of positive expression were observed in melanomas (59.0%) followed by prostate (58.0%) and lung (57.0%) tumors. CTSP-1 is part of a highly conserved gene family, and members of this family also have a restricted expression pattern and similar protein structure. Antibodies against members of this gene family were detected in 10% (14 of 141) of plasma samples from patients with a wide spectrum of tumors. The highest percentages of antibody response were observed in patients with prostate (20.8%), thyroid (20.0%), and breast (16.6%) tumors. Because of its very restricted expression pattern in normal tissues and immunogenicity in different types of tumors, CTSP-1 should be considered a promising candidate for cancer immunotherapy.
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Affiliation(s)
| | - Fabiana Bettoni
- *Ludwig Institute for Cancer Research, SP 01509-010, São Paulo, Brazil
| | - Maria D. Vibranovski
- *Ludwig Institute for Cancer Research, SP 01509-010, São Paulo, Brazil
- Biochemistry Department, University of São Paulo, SP 05508-900, São Paulo, Brazil
| | - Marilene H. Lopes
- *Ludwig Institute for Cancer Research, SP 01509-010, São Paulo, Brazil
| | | | - Isabela W. Cunha
- Pathology Department, Hospital A. C. Camargo, São Paulo, SP 01509-010, Brazil; and
| | - Fernando A. Soares
- Pathology Department, Hospital A. C. Camargo, São Paulo, SP 01509-010, Brazil; and
| | - Andrew J. G. Simpson
- Ludwig Institute for Cancer Research, Memorial Sloan–Kettering Cancer Center, New York, NY 10158
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23
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Clarizia AD, Bastos-Rodrigues L, Pena HB, Anacleto C, Rossi B, Soares FA, Lopes A, Rocha JCC, Caballero O, Camargo A, Simpson AJG, Pena SDJ. Relationship of the methylenetetrahydrofolate reductase C677T polymorphism with microsatellite instability and promoter hypermethylation in sporadic colorectal cancer. Genet Mol Res 2006; 5:315-22. [PMID: 16819711] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
The methylenetetrahydrofolate reductase (MTHFR) C677T polymorphism is associated with the expression of a thermolabile enzyme with decreased activity that influences the pool of methyl-donor molecules. Several studies have reported an association between C677T polymorphism and susceptibility to colorectal cancer (CRC). Considering that methylation abnormalities appear to be important for the pathogenesis of CRC, we examined the correlation between the genotype of the MTHFR C677T polymorphism, hypermethylation of the promoter region of five relevant genes (DAPK, MGMT, hMLH1, p16(INK4a), and p14(ARF)), and microsatellite instability, in 106 patients with primary CRCs in Brazil. We did not find significant differences in the genotypic frequencies of the MTHFR C677T polymorphism when one or more loci were hypermethylated. However, we did find a significant excess of 677TT individuals among patients with CRC who had microsatellite instability. This strong association was independent of the methylation status of hMLH1 and of the biogeographical genomic ancestry of the patients. Although the mechanism responsible for the link between the C677T polymorphism and microsatellite instability was not apparent, this finding may provide a clue towards a better understanding of the pathogenesis of microsatellite instability in human colorectal cancer.
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Affiliation(s)
- Alessandra D Clarizia
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brasil
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24
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Hicks AM, Riedlinger G, Willingham MC, Alexander-Miller MA, Von Kap-Herr C, Pettenati MJ, Sanders AM, Weir HM, Du W, Kim J, Simpson AJG, Old LJ, Cui Z. Transferable anticancer innate immunity in spontaneous regression/complete resistance mice. Proc Natl Acad Sci U S A 2006; 103:7753-8. [PMID: 16682640 PMCID: PMC1458507 DOI: 10.1073/pnas.0602382103] [Citation(s) in RCA: 115] [Impact Index Per Article: 6.4] [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: 11/18/2022] Open
Abstract
Spontaneous regression/complete resistance (SR/CR) mice resist very high doses of cancer cells that are lethal to WT mice even at low doses. In this study, we show that this resistance is mediated by rapid infiltration of leukocytes, mostly of innate immunity, in both primary and repeated challenges. Formation of rosettes with infiltrating natural killer cells, neutrophils, and macrophages was required for the subsequent destruction of cancer cells through rapid cytolysis. Highly purified natural killer cells, macrophages, and neutrophils from the SR/CR mice independently killed cancer cells in vitro. The independent killing activity by each subset of effector cells is consistent with the observation that the resistance was abolished by depleting total infiltrating leukocytes but not by depleting only one or two subsets of leukocytes. The resistance was completely transferable to WT recipient mice through SR/CR splenocytes, bone marrow cells, or enriched peritoneal macrophages, either for prevention against subsequent cancer challenges or eradication of established malignancy at distant sites.
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Affiliation(s)
| | | | | | | | - C. Von Kap-Herr
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, NC 27157; and
| | - Mark J. Pettenati
- Department of Pediatrics, Section on Medical Genetics, Wake Forest University School of Medicine, Winston-Salem, NC 27157; and
| | | | | | - Wei Du
- Departments of *Pathology
| | | | | | - Lloyd J. Old
- Ludwig Institute for Cancer Research, New York, NY 10158
- To whom correspondence may be addressed. E-mail:
or
| | - Zheng Cui
- Departments of *Pathology
- To whom correspondence may be addressed. E-mail:
or
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25
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Zhuang R, Zhu Y, Fang L, Liu XS, Tian Y, Chen LH, Ouyang WM, Xu XG, Jian JL, Güre AO, Fortunato S, Ritter G, Old LJ, Simpson AJG, Chen YT, Jin B, Jungbluth AA. Generation of monoclonal antibodies to cancer/testis (CT) antigen CT10/MAGE-C2. Cancer Immun 2006; 6:7. [PMID: 16594646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 01/19/2006] [Accepted: 01/27/2006] [Indexed: 05/08/2023]
Abstract
CT10/MAGE-C2 is a recently identified antigen that, typically of cancer/testis (CT) antigens, can be found in various malignant tumors and in normal adult testis. As with many other CT antigens, our knowledge is based mainly on mRNA expression data. In the present study, we describe the generation of mAbs to CT10/MAGE-C2 for the analysis of its protein expression. Newly generated clones were chosen based on their reactivity in ELISA, immunoblotting, and immunohistochemistry (IHC). Emphasis was put on the reactivity of newly generated reagents on formalin-fixed, paraffin-embedded tissue to ensure their applicability to archival material. Eventually we selected two clones, LX-CT10.5 and LX-CT10.9, that showed intense reactivity to CT10/MAGE-C2 protein and CT10/MAGE-C2 mRNA-positive cell lines, but no cross-reactivity with other CT antigens. Both mAbs show superior staining characteristics in IHC and are applicable to frozen and paraffin sections. In testis, CT10/MAGE-C2 displays the typical CT pattern with regard to staining of germ cells, which is intense during the early maturation stages. In tumors, we analyzed a limited number of cases displaying the typical heterogeneous CT expression pattern. Interestingly, immunoreactivity was seen solely in the nucleus: No staining was seen in the cytoplasm of tumor cells.
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Affiliation(s)
- Ran Zhuang
- Department of Immunology, Fourth Military Medical University, Xi'an 710032, PR China
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26
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Wang X, Zhao H, Xu Q, Jin W, Liu C, Zhang H, Huang Z, Zhang X, Zhang Y, Xin D, Simpson AJG, Old LJ, Na Y, Zhao Y, Chen W. HPtaa database-potential target genes for clinical diagnosis and immunotherapy of human carcinoma. Nucleic Acids Res 2006; 34:D607-12. [PMID: 16381942 PMCID: PMC1347445 DOI: 10.1093/nar/gkj082] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/02/2022] Open
Abstract
Tumor-associated antigens (TAAs) have been the most actively employed targets in the clinical diagnosis and treatment of human carcinoma, such as PSA in the diagnosis of prostate cancer and NY-ESO-1 in the immunotherapy of melanoma and other cancers. However, identification of TAAs has often been hampered by the complicated and laborsome laboratory procedures. In order to accelerate the process of tumor antigen discovery, and thereby improve diagnosis and treatment of human carcinoma, we have made an effort to establish a publicly available Human Potential Tumor Associated Antigen database (HPtaa) with potential TAAs identified by in silico computing (). Tumor specificity was chosen as the core of tumor antigen evaluation, together with other relevant clues. Various platforms of gene expression, including microarray, expressed sequence tag and SAGE data, were processed and integrated by several penalty algorithms. A total of 3518 potential TAAs have been included in the database, which is freely available to academic users. As far as we know, this database is the first one addressing human potential TAAs, and the first one integrating various kinds of expression platforms for one purpose.
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Affiliation(s)
- Xiaosong Wang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science CenterBeijing 100083, China
- Department of Urology, First Hospital of Peking University, Institute of Urology, Peking UniversityBeijing 100034, China
| | - Haitao Zhao
- Department of General Surgery, Peking Union Medical College Hospital, Chinese Academy of Medical SciencesBeijing 100032, China
| | - Qingwen Xu
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science CenterBeijing 100083, China
| | - Weibo Jin
- Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing TechnologyBeijing 100080, China
| | - Changning Liu
- Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing TechnologyBeijing 100080, China
| | - Huagang Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science CenterBeijing 100083, China
| | - Zhibin Huang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science CenterBeijing 100083, China
| | - Xinyu Zhang
- Department of Biological Science and Biotechnology, Ministry of Education Key Laboratory of Bioinformatics, Tsinghua UniversityBeijing 100084, China
| | - Yu Zhang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science CenterBeijing 100083, China
| | - Dianqi Xin
- Department of Urology, First Hospital of Peking University, Institute of Urology, Peking UniversityBeijing 100034, China
| | - Andrew J. G. Simpson
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan–Kettering Cancer CenterNew York, NY 10021, USA
| | - Lloyd J. Old
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan–Kettering Cancer CenterNew York, NY 10021, USA
| | - Yanqun Na
- Department of Urology, First Hospital of Peking University, Institute of Urology, Peking UniversityBeijing 100034, China
| | - Yi Zhao
- Bioinformatics Research Group, Key Laboratory of Intelligent Information Processing, Institute of Computing TechnologyBeijing 100080, China
| | - Weifeng Chen
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science CenterBeijing 100083, China
- To whom correspondence should be addressed. Tel: +86 10 8280 2593; Fax: +86 10 8280 1436;
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27
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Chen YT, Iseli C, Venditti CA, Old LJ, Simpson AJG, Jongeneel CV. Identification of a new cancer/testis gene family, CT47
, among expressed multicopy genes on the human X chromosome. Genes Chromosomes Cancer 2005; 45:392-400. [PMID: 16382448 DOI: 10.1002/gcc.20298] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
Abstract
Cancer/testis (CT) genes are normally expressed in germ cells only, yet are reactivated and expressed in some tumors. Of the approximately 40 CT genes or gene families identified to date, 20 are on the X chromosome and are present as multigene families, many with highly conserved members. This indicates that novel CT gene families may be identified by detecting duplicated expressed genes on chromosome X. By searching for transcript clusters that map to multiple locations on the chromosome, followed by in silico analysis of their gene expression profiles, we identified five novel gene families with testis-specific expression and >98% sequence identity among family members. The expression of these genes in normal tissues and various tumor cell lines and specimens was evaluated by qualitative and quantitative RT-PCR, and a novel CT gene family with at least 13 copies was identified on Xq24, designated as CT47. mRNA expression of CT47 was found mainly in the testes, with weak expression in the placenta. Brain tissue was the only positive somatic tissue tested, with an estimated CT47 transcript level 0.09% of that found in testis. Among the tumor specimens tested, CT47 expression was found in approximately 15% of lung cancer and esophageal cancer specimens, but not in colorectal cancer or breast cancer. The putative CT47 protein consists of 288 amino acid residues, with a C-terminus rich in alanine and glutamic acid. The only species other than human in which a gene homologous to CT47 has been detected is the chimpanzee, with the predicted protein showing approximately 80% identity in its carboxy terminal region.
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Affiliation(s)
- Yao-Tseng Chen
- Weill Medical College of Cornell University, New York, New York 10021, USA.
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Gure AO, Chua R, Williamson B, Gonen M, Ferrera CA, Gnjatic S, Ritter G, Simpson AJG, Chen YT, Old LJ, Altorki NK. Cancer-Testis Genes Are Coordinately Expressed and Are Markers of Poor Outcome in Non–Small Cell Lung Cancer. Clin Cancer Res 2005; 11:8055-62. [PMID: 16299236 DOI: 10.1158/1078-0432.ccr-05-1203] [Citation(s) in RCA: 267] [Impact Index Per Article: 14.1] [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: 11/16/2022]
Abstract
PURPOSE Cancer-testis genes mapping to the X chromosome have common expression patterns and show similar responses to modulators of epigenetic mechanisms. We asked whether cancer-testis gene expression occurred coordinately, and whether it correlated with variables of disease and clinical outcome of non-small cell lung cancer (NSCLC). EXPERIMENTAL DESIGN Tumors from 523 NSCLC patients undergoing surgery were evaluated for the expression of nine cancer-testis genes (NY-ESO-1, LAGE-1, MAGE-A1, MAGE-A3, MAGE-A4, MAGE-A10, CT7/MAGE-C1, SSX2, and SSX4) by semiquantitative PCR. Clinical data available for 447 patients were used to correlate cancer-testis expression to variables of disease and clinical outcome. RESULTS At least one cancer-testis gene was expressed by 90% of squamous carcinoma, 62% of bronchioloalveolar cancer, and 67% of adenocarcinoma samples. Statistically significant coexpression was observed for 34 of the 36 possible cancer-testis combinations. Cancer-testis gene expression, either cumulatively or individually, showed significant associations with male sex, smoking history, advanced tumor, nodal and pathologic stages, pleural invasion, and the absence of ground glass opacity. Cox regression analysis revealed the expression of NY-ESO-1 and MAGE-A3 as markers of poor prognosis, independent of confounding variables for adenocarcinoma of the lung. CONCLUSIONS Cancer-testis genes are coordinately expressed in NSCLC, and their expression is associated with advanced disease and poor outcome.
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Affiliation(s)
- Ali O Gure
- Ludwig Institute for Cancer Research, Memorial Sloan Kettering Cancer Center, New York, New York 10021, USA.
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Rand V, Huang J, Stockwell T, Ferriera S, Buzko O, Levy S, Busam D, Li K, Edwards JB, Eberhart C, Murphy KM, Tsiamouri A, Beeson K, Simpson AJG, Venter JC, Riggins GJ, Strausberg RL. Sequence survey of receptor tyrosine kinases reveals mutations in glioblastomas. Proc Natl Acad Sci U S A 2005; 102:14344-9. [PMID: 16186508 PMCID: PMC1242336 DOI: 10.1073/pnas.0507200102] [Citation(s) in RCA: 121] [Impact Index Per Article: 6.4] [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: 12/11/2022] Open
Abstract
It is now clear that tyrosine kinases represent attractive targets for therapeutic intervention in cancer. Recent advances in DNA sequencing technology now provide the opportunity to survey mutational changes in cancer in a high-throughput and comprehensive manner. Here we report on the sequence analysis of members of the receptor tyrosine kinase (RTK) gene family in the genomes of glioblastoma brain tumors. Previous studies have identified a number of molecular alterations in glioblastoma, including amplification of the RTK epidermal growth factor receptor. We have identified mutations in two other RTKs: (i) fibroblast growth receptor 1, including the first mutations in the kinase domain in this gene observed in any cancer, and (ii) a frameshift mutation in the platelet-derived growth factor receptor-alpha gene. Fibroblast growth receptor 1, platelet-derived growth factor receptor-alpha, and epidermal growth factor receptor are all potential entry points to the phosphatidylinositol 3-kinase and mitogen-activated protein kinase intracellular signaling pathways already known to be important for neoplasia. Our results demonstrate the utility of applying DNA sequencing technology to systematically assess the coding sequence of genes within cancer genomes.
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Affiliation(s)
- Vikki Rand
- Department of Neurosurgery, Johns Hopkins University School of Medicine, 5200 Eastern Avenue, Baltimore, MD 21224, USA
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Anacleto C, Leopoldino AM, Rossi B, Soares FA, Lopes A, Rocha JCC, Caballero O, Camargo AA, Simpson AJG, Pena SDJ. Colorectal cancer "methylator phenotype": fact or artifact? Neoplasia 2005; 7:331-5. [PMID: 15967110 PMCID: PMC1501152 DOI: 10.1593/neo.04502] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2004] [Revised: 11/21/2004] [Accepted: 11/23/2004] [Indexed: 01/28/2023] Open
Abstract
It has been proposed that human colorectal tumors can be classified into two groups: one in which methylation is rare, and another with methylation of several loci associated with a "CpG island methylated phenotype (CIMP)," characterized by preferential proximal location in the colon, but otherwise poorly defined. There is considerable overlap between this putative methylator phenotype and the well-known mutator phenotype associated with microsatellite instability (MSI). We have examined hypermethylation of the promoter region of five genes (DAPK, MGMT, hMLH1, p16INK4a, and p14ARF) in 106 primary colorectal cancers. A graph depicting the frequency of methylated loci in the series of tumors showed a continuous, monotonically decreasing distribution quite different from the previously claimed discontinuity. We observed a significant association between the presence of three or more methylated loci and the proximal location of the tumors. However, if we remove from analysis the tumors with hMLH1 methylation or those with MSI, the significance vanishes, suggesting that the association between multiple methylations and proximal location was indirect due to the correlation with MSI. Thus, our data do not support the independent existence of the so-called methylator phenotype and suggest that it rather may represent a statistical artifact caused by confounding of associations.
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Affiliation(s)
- Charles Anacleto
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, 31270-910 Brazil
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Jongeneel CV, Delorenzi M, Iseli C, Zhou D, Haudenschild CD, Khrebtukova I, Kuznetsov D, Stevenson BJ, Strausberg RL, Simpson AJG, Vasicek TJ. An atlas of human gene expression from massively parallel signature sequencing (MPSS). Genome Res 2005; 15:1007-14. [PMID: 15998913 PMCID: PMC1172045 DOI: 10.1101/gr.4041005] [Citation(s) in RCA: 133] [Impact Index Per Article: 7.0] [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: 11/24/2022]
Abstract
We have used massively parallel signature sequencing (MPSS) to sample the transcriptomes of 32 normal human tissues to an unprecedented depth, thus documenting the patterns of expression of almost 20,000 genes with high sensitivity and specificity. The data confirm the widely held belief that differences in gene expression between cell and tissue types are largely determined by transcripts derived from a limited number of tissue-specific genes, rather than by combinations of more promiscuously expressed genes. Expression of a little more than half of all known human genes seems to account for both the common requirements and the specific functions of the tissues sampled. A classification of tissues based on patterns of gene expression largely reproduces classifications based on anatomical and biochemical properties. The unbiased sampling of the human transcriptome achieved by MPSS supports the idea that most human genes have been mapped, if not functionally characterized. This data set should prove useful for the identification of tissue-specific genes, for the study of global changes induced by pathological conditions, and for the definition of a minimal set of genes necessary for basic cell maintenance. The data are available on the Web at http://mpss.licr.org and http://sgb.lynxgen.com.
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Affiliation(s)
- C Victor Jongeneel
- Office of Information Technology, Ludwig Institute for Cancer Research, and Swiss Institute of Bioinformatics, 1015 Lausanne, Switzerland.
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Vural B, Chen LC, Saip P, Chen YT, Ustuner Z, Gonen M, Simpson AJG, Old LJ, Ozbek U, Gure AO. Frequency of SOX Group B (SOX1, 2, 3) and ZIC2 antibodies in Turkish patients with small cell lung carcinoma and their correlation with clinical parameters. Cancer 2005; 103:2575-83. [PMID: 15880380 DOI: 10.1002/cncr.21088] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.1] [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: 01/02/2023]
Abstract
BACKGROUND Expression of neuroectodermal markers is a key feature of small cell lung carcinoma (SCLC). Although immune responses against a number of these proteins have been associated with paraneoplastic neuronal disease (PND), most patients with SCLC have anti-neuroectodermal antibodies in the absence of PND. Whether these immune responses affect the clinical outcome in SCLC is critical in understanding the potential value of these proteins as cancer vaccine targets as well as in the pathogenesis of PND. METHODS The authors investigated the frequency of immunoglobulin G autoantibodies against Sry-like high-mobility group box (SOX)1, 2, 3 and Zinc-finger gene of the cerebellum (ZIC)2 proteins in stored serum samples from 90 patients utilizing the lambda-phage plaque assay. Data obtained from patient records were utilized to measure clinical correlates of seroreactivity. RESULTS Antibodies to SOX1 were present in 28% of patients and another 28% had anti-ZIC2 antibodies, classifying these as some of the most frequent antibody responses observed in SCLC. None had autoimmune paraneoplastic disease. Antibody titers were frequently as high as > or = 1:10(6) and were stable for < or = 6 months after diagnosis. Seroreactivity against either SOX1 or ZIC2 correlated with younger age, lower lactate dehydrogenase levels, and better response to initial therapy. CONCLUSIONS The frequent and stable presence of SOX Group B and/or ZIC2 antibodies in SCLC, but not in healthy individuals examined, indicates they are serological markers of SCLC. However, the correlation between known clinical parameters of less aggressive disease and seroreactivity suggests that these antibodies are indicators of better prognosis in SCLC and warrants further studies to clarify the nature of the underlying immune responses.
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Affiliation(s)
- Burcak Vural
- Department of Genetics, Institute for Experimental Research, Istanbul University, Istanbul, Turkey
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Vasconcelos ATR, Ferreira HB, Bizarro CV, Bonatto SL, Carvalho MO, Pinto PM, Almeida DF, Almeida LGP, Almeida R, Alves-Filho L, Assunção EN, Azevedo VAC, Bogo MR, Brigido MM, Brocchi M, Burity HA, Camargo AA, Camargo SS, Carepo MS, Carraro DM, de Mattos Cascardo JC, Castro LA, Cavalcanti G, Chemale G, Collevatti RG, Cunha CW, Dallagiovanna B, Dambrós BP, Dellagostin OA, Falcão C, Fantinatti-Garboggini F, Felipe MSS, Fiorentin L, Franco GR, Freitas NSA, Frías D, Grangeiro TB, Grisard EC, Guimarães CT, Hungria M, Jardim SN, Krieger MA, Laurino JP, Lima LFA, Lopes MI, Loreto ELS, Madeira HMF, Manfio GP, Maranhão AQ, Martinkovics CT, Medeiros SRB, Moreira MAM, Neiva M, Ramalho-Neto CE, Nicolás MF, Oliveira SC, Paixão RFC, Pedrosa FO, Pena SDJ, Pereira M, Pereira-Ferrari L, Piffer I, Pinto LS, Potrich DP, Salim ACM, Santos FR, Schmitt R, Schneider MPC, Schrank A, Schrank IS, Schuck AF, Seuanez HN, Silva DW, Silva R, Silva SC, Soares CMA, Souza KRL, Souza RC, Staats CC, Steffens MBR, Teixeira SMR, Urmenyi TP, Vainstein MH, Zuccherato LW, Simpson AJG, Zaha A. Swine and poultry pathogens: the complete genome sequences of two strains of Mycoplasma hyopneumoniae and a strain of Mycoplasma synoviae. J Bacteriol 2005; 187:5568-77. [PMID: 16077101 PMCID: PMC1196056 DOI: 10.1128/jb.187.16.5568-5577.2005] [Citation(s) in RCA: 221] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2005] [Accepted: 05/19/2005] [Indexed: 11/20/2022] Open
Abstract
This work reports the results of analyses of three complete mycoplasma genomes, a pathogenic (7448) and a nonpathogenic (J) strain of the swine pathogen Mycoplasma hyopneumoniae and a strain of the avian pathogen Mycoplasma synoviae; the genome sizes of the three strains were 920,079 bp, 897,405 bp, and 799,476 bp, respectively. These genomes were compared with other sequenced mycoplasma genomes reported in the literature to examine several aspects of mycoplasma evolution. Strain-specific regions, including integrative and conjugal elements, and genome rearrangements and alterations in adhesin sequences were observed in the M. hyopneumoniae strains, and all of these were potentially related to pathogenicity. Genomic comparisons revealed that reduction in genome size implied loss of redundant metabolic pathways, with maintenance of alternative routes in different species. Horizontal gene transfer was consistently observed between M. synoviae and Mycoplasma gallisepticum. Our analyses indicated a likely transfer event of hemagglutinin-coding DNA sequences from M. gallisepticum to M. synoviae.
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Affiliation(s)
- Ana Tereza R Vasconcelos
- Centro de Biotecnologia, Universidade Federal do Rio Grande do Sul, Avenida Bento Gonçalves 9500, Prédio 43421, Porto Alegre, RS, Brazil
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Abstract
Cancer/testis (CT) antigens, of which more than 40 have now been identified, are encoded by genes that are normally expressed only in the human germ line, but are also expressed in various tumour types, including melanoma, and carcinomas of the bladder, lung and liver. These immunogenic proteins are being vigorously pursued as targets for therapeutic cancer vaccines. CT antigens are also being evaluated for their role in oncogenesis--recapitulation of portions of the germline gene-expression programme might contribute characteristic features to the neoplastic phenotype, including immortality, invasiveness, immune evasion, hypomethylation and metastatic capacity.
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Affiliation(s)
- Andrew J G Simpson
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, New York 10021, USA.
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35
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Chen YT, Venditti CA, Theiler G, Stevenson BJ, Iseli C, Gure AO, Jongeneel CV, Old LJ, Simpson AJG. Identification of CT46/HORMAD1, an immunogenic cancer/testis antigen encoding a putative meiosis-related protein. Cancer Immun 2005; 5:9. [PMID: 15999985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 04/21/2005] [Accepted: 06/06/2005] [Indexed: 05/03/2023]
Abstract
Transcripts with ESTs derived exclusively or predominantly from testis, and not from other normal tissues, are likely to be products of genes with testis-restricted expression, and are thus potential cancer/testis (CT) antigen genes. A list of 371 genes with such characteristics was compiled by analyzing publicly available EST databases. RT-PCR analysis of normal and tumor tissues was performed to validate an initial selection of 20 of these genes. Several new CT and CT-like genes were identified. One of these, CT46/HORMAD1, is expressed strongly in testis and weakly in placenta; the highest level of expression in other tissues is <1% of testicular expression. The CT46/HORMAD1 gene was expressed in 31% (34/109) of the carcinomas examined, with 11% (12/109) showing expression levels >10% of the testicular level of expression. CT46/HORMAD1 is a single-copy gene on chromosome 1q21.3, encoding a putative protein of 394 aa. Conserved protein domain analysis identified a HORMA domain involved in chromatin binding. The CT46/HORMAD1 protein was found to be homologous to the prototype HORMA domain-containing protein, Hop1, a yeast meiosis-specific protein, as well as to asy1, a meiotic synaptic mutant protein in Arabidopsis thaliana.
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Affiliation(s)
- Yao-Tseng Chen
- Weill Medical College, Cornell University, New York, NY 10021, USA
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36
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Chen YT, Scanlan MJ, Venditti CA, Chua R, Theiler G, Stevenson BJ, Iseli C, Gure AO, Vasicek T, Strausberg RL, Jongeneel CV, Old LJ, Simpson AJG. Identification of cancer/testis-antigen genes by massively parallel signature sequencing. Proc Natl Acad Sci U S A 2005; 102:7940-5. [PMID: 15905330 PMCID: PMC1142383 DOI: 10.1073/pnas.0502583102] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [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: 01/29/2023] Open
Abstract
Massively parallel signature sequencing (MPSS) generates millions of short sequence tags corresponding to transcripts from a single RNA preparation. Most MPSS tags can be unambiguously assigned to genes, thereby generating a comprehensive expression profile of the tissue of origin. From the comparison of MPSS data from 32 normal human tissues, we identified 1,056 genes that are predominantly expressed in the testis. Further evaluation by using MPSS tags from cancer cell lines and EST data from a wide variety of tumors identified 202 of these genes as candidates for encoding cancer/testis (CT) antigens. Of these genes, the expression in normal tissues was assessed by RT-PCR in a subset of 166 intron-containing genes, and those with confirmed testis-predominant expression were further evaluated for their expression in 21 cancer cell lines. Thus, 20 CT or CT-like genes were identified, with several exhibiting expression in five or more of the cancer cell lines examined. One of these genes is a member of a CT gene family that we designated as CT45. The CT45 family comprises six highly similar (>98% cDNA identity) genes that are clustered in tandem within a 125-kb region on Xq26.3. CT45 was found to be frequently expressed in both cancer cell lines and lung cancer specimens. Thus, MPSS analysis has resulted in a significant extension of our knowledge of CT antigens, leading to the discovery of a distinctive X-linked CT-antigen gene family.
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Affiliation(s)
- Yao-Tseng Chen
- Weill Medical College of Cornell University, New York, NY 10021, USA.
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Shang XY, Chen HS, Zhang HG, Pang XW, Qiao H, Peng JR, Qin LL, Fei R, Mei MH, Leng XS, Gnjatic S, Ritter G, Simpson AJG, Old LJ, Chen WF. The spontaneous CD8+ T-cell response to HLA-A2-restricted NY-ESO-1b peptide in hepatocellular carcinoma patients. Clin Cancer Res 2005; 10:6946-55. [PMID: 15501973 DOI: 10.1158/1078-0432.ccr-04-0502] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
PURPOSE Hepatocellular carcinoma (HCC) can express various cancer-testis antigens including NY-ESO-1, members of the SSX family, members of the MAGE family, SCP-1, and CTP11. Immunotherapy directed against these antigens is a potential alternative treatment for HCC. To date, it remains unclear whether HCC patients have spontaneous immune responses to these tumor antigens. The objectives of this study were to measure immune responses to NY-ESO-1, a promising cancer vaccine candidate, in HCC patients using the HLA-A2-restricted NY-ESO-1b peptide (p157-165) to measure cellular responses and whole protein to measure antibody responses. EXPERIMENTAL DESIGN In HLA-A2(+) patients with NY-ESO-1(+) HCC, we analyzed T-cell antigen-dependent interferon (IFN)-gamma and/or Granzyme B release by enzyme-linked immunospot (ELISPOT) assay and IFN-gamma-producing intracellular cytokine flow cytometry (CytoSpot). As an assay independent of T-cell function, we performed tetramer staining. Antibodies to whole NY-ESO-1 were assayed by enzyme-linked immunosorbent assay. RESULTS The frequency of specific CD8(+) T-cell responses to NY-ESO-1b in 28 NY-ESO-1 mRNA(+)HLA-A2(+) HCC patients was 35.7% (10 of 28). The average magnitude of effector CD8(+) T cells was 0.3% (89 +/- 59 per 2.5 x 10(4) CD8(+) cells) and 1.2% as measured by IFN-gamma release ELISPOT and CytoSpot assays, respectively. These in vitro induced NY-ESO-1b-specific CD8(+) T cells can also recognize HepG2 cells transfected with pcDNA3.1-NY-ESO-1 in both IFN-gamma and Granzyme B ELISPOT assays. Frequencies of NY-ESO-1b-specific T cells in several patients were confirmed by tetramer staining. Nonfunctional tetramer(+)CD8(+) T cells were also present. The CD8(+) T-cell response was apparently increased in patients with late-stage HCC. A discordance between antibody and CD8(+) T-cell responses in HCC patients was observed. CONCLUSIONS The elevated frequency of specific CD8(+) T-cell responses to NY-ESO-1b in NY-ESO-1 mRNA(+)HLA-A2(+) HCC patients suggests that NY-ESO-1 is appropriate for use in the immunotherapy of HCC patients.
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Affiliation(s)
- Xiao-Ying Shang
- Department of Immunology, School of Basic Medical Sciences, Peking University Health Science Center, Beijing, People's Republic of China
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38
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Anacleto C, Rossi B, Lopes A, Soares FA, Rocha JCC, Caballero O, Camargo AA, Simpson AJG, Pena SDJ. Development and application of a multiplex PCR procedure for the detection of DNA methylation in colorectal cancer. Oncol Rep 2005; 13:325-8. [PMID: 15643519] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023] Open
Abstract
Cancers often exhibit aberrant methylation of gene promoter regions associated with loss of tumor suppressor and/or DNA repair gene function. Such methylation constitutes an excellent marker for the molecular detection of micro-metastases and the diagnosis of tumor recurrences. We have developed a multiplex methylation-specific PCR (MSP) procedure for rapid and simultaneous assessment of the methylation of 5 loci: the tumor suppressor genes p16INK4a, death-associated protein kinase (DAPK) and p14ARF, and the DNA repair genes hMLH1 and O6-methylguanine-DNA-methyltransferase (MGMT). This multiplex test uses one single PCR reaction and only one electrophoretic run. In 98 samples of colorectal cancer studied, methylation of MGMT, DAPK, p16, hMLH1 and p14 was present in 31, 20, 17, 16 and 14% of tumors, respectively. In 58% of the tumors at least one methylated gene was found. This multiplex MSP constitutes a simple and inexpensive method for screening of molecular signatures in colorectal cancer and can be used profitably before employing more expensive and complex techniques such as microarray testing.
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Affiliation(s)
- Charles Anacleto
- Departamento de Bioquímica e Imunologia, Universidade Federal de Minas Gerais, Belo Horizonte, MG, Brazil
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Ferreira EN, Pires LC, Parmigiani RB, Bettoni F, Puga RD, Pinheiro DG, Andrade LEC, Cruz LO, Degaki TL, Faria M, Festa F, Giannella-Neto D, Giorgi RR, Goldman GH, Granja F, Gruber A, Hackel C, Henrique-Silva F, Malnic B, Manzini CVB, Marie SKN, Martinez-Rossi NM, Oba-Shinjo SM, Pardini MIMC, Rahal P, Rainho CA, Rogatto SR, Romano CM, Rodrigues V, Sales MM, Savoldi M, da Silva IDCG, da Silva NP, de Souza SJ, Tajara EH, Silva WA, Simpson AJG, Sogayar MC, Camargo AA, Carraro DM. Identification and complete sequencing of novel human transcripts through the use of mouse orthologs and testis cDNA sequences. Genet Mol Res 2004; 3:493-511. [PMID: 15688316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
The correct identification of all human genes, and their derived transcripts, has not yet been achieved, and it remains one of the major aims of the worldwide genomics community. Computational programs suggest the existence of 30,000 to 40,000 human genes. However, definitive gene identification can only be achieved by experimental approaches. We used two distinct methodologies, one based on the alignment of mouse orthologous sequences to the human genome, and another based on the construction of a high-quality human testis cDNA library, in an attempt to identify new human transcripts within the human genome sequence. We generated 47 complete human transcript sequences, comprising 27 unannotated and 20 annotated sequences. Eight of these transcripts are variants of previously known genes. These transcripts were characterized according to size, number of exons, and chromosomal localization, and a search for protein domains was undertaken based on their putative open reading frames. In silico expression analysis suggests that some of these transcripts are expressed at low levels and in a restricted set of tissues.
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Affiliation(s)
- Elisa N Ferreira
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, São Paulo, SP, Brazil
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Lopes LF, Piccoli FDS, Paixão VA, Latorre MDRDO, Camargo BD, Simpson AJG, Caballero OL. Association of CYP3A4 genotype with detection of Vγ/Jβ trans-rearrangements in the peripheral blood leukocytes of pediatric cancer patients undergoing chemotherapy for ALL. Leuk Res 2004; 28:1281-6. [PMID: 15475069 DOI: 10.1016/j.leukres.2004.04.014] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2003] [Accepted: 04/20/2004] [Indexed: 11/19/2022]
Abstract
Cancer patients receiving chemotherapy are exposed to high doses of cytotoxic and genotoxic drugs which, in some cases, can lead to treatment related leukemia. Since this only occurs in a minority of patients, however, it is possible some individuals are predisposed due to genetic polymorphisms in genes for enzymes that mediate drug metabolism. To address this possibility we measured the genotoxicity of chemotherapeutic agents in patients receiving treatment for ALL by the frequency of the Vgamma/Jbeta trans-rearrangement in their peripheral blood leukocytes and compared this with CYP3A4 genotype. CYP3A4 is the most abundant of the cytochrome P450 (CYP) enzyme in the liver and intestine which contains a common -392A>G substitution in the promoter region (CYP3A4*1B allele). We found a significant increase in the frequency of rearrangements during chemotherapy only in patients homozygous for the wild type CYP3A4*1A allele. This provides a direct link between CYP3A4 genotype and susceptibility to drug genotoxicity thus strengthening the possibility that predisposition to treatment related leukemia may be measurable by simple genetic testing.
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Affiliation(s)
- Luiz Fernando Lopes
- Pediatric Department, Centro de Tratamento e Pesquisa Hospital do Cancer Rua Prof. Antônio Prudente, 211 CEP 04038-002 São Paulo, SP, Brazil.
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41
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Lee SY, Williamson B, Caballero OL, Chen YT, Scanlan MJ, Ritter G, Jongeneel CV, Simpson AJG, Old LJ. Identification of the gonad-specific anion transporter SLCO6A1 as a cancer/testis (CT) antigen expressed in human lung cancer. Cancer Immun 2004; 4:13. [PMID: 15546177] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Received: 06/03/2004] [Accepted: 07/09/2004] [Indexed: 05/01/2023]
Abstract
Serological analysis of recombinant cDNA expression libraries (SEREX) has led to the identification of many of the antigens recognized by the immune system of cancer patients, which are collectively referred to as the cancer immunome. We used SEREX to screen a testicular cDNA expression library with sera obtained from non-small cell lung cancer patients and isolated cDNA clones for 82 antigens. These included a total of 31 antigens previously identified by SEREX, and 51 that did not match entries in the Cancer Immunome Database and were considered newly identified antigens. Overall, the antigens comprised 62 known proteins and 20 uncharacterized gene products. Six antigens (NY-TLU-6, -37, -39, -57, -70, -75) were identified as putative cell surface proteins that are potential targets for monoclonal antibody-based immunotherapy. Of these, the gonad-specific anion transport protein SLCO6A1 (NY-TLU-57) was shown to be tissue-restricted. RT-PCR showed it to be expressed strongly only in normal testis, and weakly in spleen, brain, fetal brain, and placenta. In addition, NY-TLU-57 mRNA was found in lung tumor samples (5/10) and lung cancer cell lines (6/11), as well as bladder (5/12) and esophageal (5/12) tumor samples. These data suggest that SLCO6A1 is a putative cancer/testis (CT) cell surface antigen of potential utility as a target for antibody-based therapy for a variety of tumor types. The analysis also permits us to estimate the eventual size of the SEREX-defined cancer immunome at around 4000 genes. This emphasizes the importance of continued SEREX screening to define the cancer immunome.
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MESH Headings
- Anion Transport Proteins/biosynthesis
- Anion Transport Proteins/genetics
- Anion Transport Proteins/immunology
- Antigens, Neoplasm/biosynthesis
- Antigens, Neoplasm/genetics
- Antigens, Neoplasm/immunology
- Carcinoma, Non-Small-Cell Lung/blood
- Carcinoma, Non-Small-Cell Lung/genetics
- Carcinoma, Non-Small-Cell Lung/immunology
- DNA, Neoplasm/blood
- DNA, Neoplasm/genetics
- Gene Library
- Humans
- Lung Neoplasms/blood
- Lung Neoplasms/genetics
- Lung Neoplasms/immunology
- Male
- Organic Anion Transporters/biosynthesis
- Organic Anion Transporters/genetics
- Organic Anion Transporters/immunology
- RNA, Messenger/biosynthesis
- RNA, Messenger/genetics
- Testis/immunology
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Affiliation(s)
- Sang-Yull Lee
- Ludwig Institute for Cancer Research, New York Branch at Memorial Sloan-Kettering Cancer Center, 1275 York Avenue, New York, NY 10021, USA
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42
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Dani MAC, Dani SU, Lima SPG, Martinez A, Rossi BM, Soares F, Zago MA, Simpson AJG. Less DeltamtDNA4977 than normal in various types of tumors suggests that cancer cells are essentially free of this mutation. Genet Mol Res 2004; 3:395-409. [PMID: 15614730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/01/2023]
Abstract
Levels of mtDNA(4977) deletions (DeltamtDNA(4977)) have been found to be lower in tumors than in adjacent non-tumoral tissues. In 87 cancer patients, DeltamtDNA(4977) was detected by multiplex polymerase chain reaction (PCR) amplification in 43 (49%) of the tumors and in 74 (85%) of the samples of non-tumoral tissues that were adjacent to the tumors. DeltamtDNA(4977) deletions were detected in 24% of the breast tumors, 52% of the colorectal tumors, 79% of the gastric tumors, and 40% of the head and neck tumors as compared with 77, 83, 100, and 90% of the adjacent respective non-tumoral tissues at the same DNA template dilution. Based on limiting dilution PCR of 16 tumors and their adjacent non-tumoral tissues, it was found that the amount of DeltamtDNA(4977) was 10- to 100-fold lower in the tumor than in the respective control non-tumoral tissues. Real-time PCR experiments were performed to quantify the number of DeltamtDNA(4977) deletions per cell, by determining the mitochondrial-to-nuclear DNA ratio. In all of the cases of breast, colorectal, gastric, and head and neck cancer the proportion of DeltamtDNA(4977) in tumors was lower than that of the respective non-tumoral tissue. Traces of DeltamtDNA(4977) in tumors were apparently due to contamination of tumor tissue with surrounding non-tumoral tissue, as evidenced by tumor microdissection and in situ PCR techniques, suggesting that tumors are essentially free of this mutation. Although the metabolic effect of DeltamtDNA(4977) may be minimal in normal (non-tumor) tissue, in tissue under stress, such as in tumors, even low levels of DeltamtDNA(4977) deletions may be intolerable.
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Affiliation(s)
- Maria Angela C Dani
- Department of Genetics, Medical School, University of São Paulo, Ribeirão Preto, SP, Brazil
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43
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Monteiro-Vitorello CB, Camargo LEA, Van Sluys MA, Kitajima JP, Truffi D, do Amaral AM, Harakava R, de Oliveira JCF, Wood D, de Oliveira MC, Miyaki C, Takita MA, da Silva ACR, Furlan LR, Carraro DM, Camarotte G, Almeida NF, Carrer H, Coutinho LL, El-Dorry HA, Ferro MIT, Gagliardi PR, Giglioti E, Goldman MHS, Goldman GH, Kimura ET, Ferro ES, Kuramae EE, Lemos EGM, Lemos MVF, Mauro SMZ, Machado MA, Marino CL, Menck CF, Nunes LR, Oliveira RC, Pereira GG, Siqueira W, de Souza AA, Tsai SM, Zanca AS, Simpson AJG, Brumbley SM, Setúbal JC. The genome sequence of the gram-positive sugarcane pathogen Leifsonia xyli subsp. xyli. Mol Plant Microbe Interact 2004; 17:827-836. [PMID: 15305603 DOI: 10.1094/mpmi.2004.17.8.827] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
The genome sequence of Leifsonia xyli subsp. xyli, which causes ratoon stunting disease and affects sugarcane worldwide, was determined. The single circular chromosome of Leifsonia xyli subsp. xyli CTCB07 was 2.6 Mb in length with a GC content of 68% and 2,044 predicted open reading frames. The analysis also revealed 307 predicted pseudogenes, which is more than any bacterial plant pathogen sequenced to date. Many of these pseudogenes, if functional, would likely be involved in the degradation of plant heteropolysaccharides, uptake of free sugars, and synthesis of amino acids. Although L. xyli subsp. xyli has only been identified colonizing the xylem vessels of sugarcane, the numbers of predicted regulatory genes and sugar transporters are similar to those in free-living organisms. Some of the predicted pathogenicity genes appear to have been acquired by lateral transfer and include genes for cellulase, pectinase, wilt-inducing protein, lysozyme, and desaturase. The presence of the latter may contribute to stunting, since it is likely involved in the synthesis of abscisic acid, a hormone that arrests growth. Our findings are consistent with the nutritionally fastidious behavior exhibited by L. xyli subsp. xyli and suggest an ongoing adaptation to the restricted ecological niche it inhabits.
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Affiliation(s)
- Claudia B Monteiro-Vitorello
- Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Av. Pádua Dias, 11, 13418-900, Piracicaba, SP, Brazil
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44
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Sogayar MC, Camargo AA, Bettoni F, Carraro DM, Pires LC, Parmigiani RB, Ferreira EN, de Sá Moreira E, do Rosário D de O Latorre M, Simpson AJG, Cruz LO, Degaki TL, Festa F, Massirer KB, Sogayar MC, Filho FC, Camargo LP, Cunha MAV, De Souza SJ, Faria M, Giuliatti S, Kopp L, de Oliveira PSL, Paiva PB, Pereira AA, Pinheiro DG, Puga RD, S de Souza JE, Albuquerque DM, Andrade LEC, Baia GS, Briones MRS, Cavaleiro-Luna AMS, Cerutti JM, Costa FF, Costanzi-Strauss E, Espreafico EM, Ferrasi AC, Ferro ES, Fortes MAHZ, Furchi JRF, Giannella-Neto D, Goldman GH, Goldman MHS, Gruber A, Guimarães GS, Hackel C, Henrique-Silva F, Kimura ET, Leoni SG, Macedo C, Malnic B, Manzini B CV, Marie SKN, Martinez-Rossi NM, Menossi M, Miracca EC, Nagai MA, Nobrega FG, Nobrega MP, Oba-Shinjo SM, Oliveira MK, Orabona GM, Otsuka AY, Paço-Larson ML, Paixão BMC, Pandolfi JRC, Pardini MIMC, Passos Bueno MR, Passos GAS, Pesquero JB, Pessoa JG, Rahal P, Rainho CA, Reis CP, Ricca TI, Rodrigues V, Rogatto SR, Romano CM, Romeiro JG, Rossi A, Sá RG, Sales MM, Sant'Anna SC, Santarosa PL, Segato F, Silva WA, Silva IDCG, Silva NP, Soares-Costa A, Sonati MF, Strauss BE, Tajara EH, Valentini SR, Villanova FE, Ward LS, Zanette DL. A transcript finishing initiative for closing gaps in the human transcriptome. Genome Res 2004; 14:1413-23. [PMID: 15197164 PMCID: PMC442158 DOI: 10.1101/gr.2111304] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2003] [Accepted: 03/12/2004] [Indexed: 11/24/2022]
Abstract
We report the results of a transcript finishing initiative, undertaken for the purpose of identifying and characterizing novel human transcripts, in which RT-PCR was used to bridge gaps between paired EST clusters, mapped against the genomic sequence. Each pair of EST clusters selected for experimental validation was designated a transcript finishing unit (TFU). A total of 489 TFUs were selected for validation, and an overall efficiency of 43.1% was achieved. We generated a total of 59,975 bp of transcribed sequences organized into 432 exons, contributing to the definition of the structure of 211 human transcripts. The structure of several transcripts reported here was confirmed during the course of this project, through the generation of their corresponding full-length cDNA sequences. Nevertheless, for 21% of the validated TFUs, a full-length cDNA sequence is not yet available in public databases, and the structure of 69.2% of these TFUs was not correctly predicted by computer programs. The TF strategy provides a significant contribution to the definition of the complete catalog of human genes and transcripts, because it appears to be particularly useful for identification of low abundance transcripts expressed in a restricted set of tissues as well as for the delineation of gene boundaries and alternatively spliced isoforms.
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Abstract
Scientists have sequenced the human genome and identified most of its genes. Now it is time to use these genomic data, and the high-throughput technology developed to generate them, to tackle major health problems such as cancer. To accelerate our understanding of this disease and to produce targeted therapies, further basic mutational and functional genomic information is required. A systematic and coordinated approach, with the results freely available, should speed up progress. This will best be accomplished through an international academic and pharmaceutical oncogenomics initiative.
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Affiliation(s)
- Robert L Strausberg
- Department of Mammalian Genomics, The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, Maryland 2085, USA.
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46
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Nascimento ALTO, Ko AI, Martins EAL, Monteiro-Vitorello CB, Ho PL, Haake DA, Verjovski-Almeida S, Hartskeerl RA, Marques MV, Oliveira MC, Menck CFM, Leite LCC, Carrer H, Coutinho LL, Degrave WM, Dellagostin OA, El-Dorry H, Ferro ES, Ferro MIT, Furlan LR, Gamberini M, Giglioti EA, Góes-Neto A, Goldman GH, Goldman MHS, Harakava R, Jerônimo SMB, Junqueira-de-Azevedo ILM, Kimura ET, Kuramae EE, Lemos EGM, Lemos MVF, Marino CL, Nunes LR, de Oliveira RC, Pereira GG, Reis MS, Schriefer A, Siqueira WJ, Sommer P, Tsai SM, Simpson AJG, Ferro JA, Camargo LEA, Kitajima JP, Setubal JC, Van Sluys MA. Comparative genomics of two Leptospira interrogans serovars reveals novel insights into physiology and pathogenesis. J Bacteriol 2004; 186:2164-72. [PMID: 15028702 PMCID: PMC374407 DOI: 10.1128/jb.186.7.2164-2172.2004] [Citation(s) in RCA: 312] [Impact Index Per Article: 15.6] [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] [Indexed: 11/20/2022] Open
Abstract
Leptospira species colonize a significant proportion of rodent populations worldwide and produce life-threatening infections in accidental hosts, including humans. Complete genome sequencing of Leptospira interrogans serovar Copenhageni and comparative analysis with the available Leptospira interrogans serovar Lai genome reveal that despite overall genetic similarity there are significant structural differences, including a large chromosomal inversion and extensive variation in the number and distribution of insertion sequence elements. Genome sequence analysis elucidates many of the novel aspects of leptospiral physiology relating to energy metabolism, oxygen tolerance, two-component signal transduction systems, and mechanisms of pathogenesis. A broad array of transcriptional regulation proteins and two new families of afimbrial adhesins which contribute to host tissue colonization in the early steps of infection were identified. Differences in genes involved in the biosynthesis of lipopolysaccharide O side chains between the Copenhageni and Lai serovars were identified, offering an important starting point for the elucidation of the organism's complex polysaccharide surface antigens. Differences in adhesins and in lipopolysaccharide might be associated with the adaptation of serovars Copenhageni and Lai to different animal hosts. Hundreds of genes encoding surface-exposed lipoproteins and transmembrane outer membrane proteins were identified as candidates for development of vaccines for the prevention of leptospirosis.
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Affiliation(s)
- A L T O Nascimento
- Centro de Biotecnologia, Instituto Butantan, Universidade de São Paulo, São Paulo, Brazil.
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Simpson AJG, Camargo AA, Ferro JA, Parra J, Vasconcelos AT. Coordinated, network-based research as a strategic component of science in Brazil. Genet Mol Res 2004; 3:18-25. [PMID: 15100985] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
Scientific research plays a fundamental role in the health and development of any society, since all technological advances depend ultimately on scientific discovery and the generation of wealth is intricately dependent on technological advance. Due to their importance, science and technology generally occupy important places in the hierarchical structure of developed societies, and they receive considerable public and private investment. Publicly funded science is almost entirely devoted to discovery, and it is administered and structured in a very similar way throughout the world. Particularly in the biological sciences, this structure, which is very much centered on the individual scientist and his own hypothesis-based investigations, may not be the best suited for either discovery in the context of complex biological systems, or for the efficient advancement of fundamental knowledge into practical utility. The adoption of other organizational paradigms, which permit a more coordinated and interactive research structure, may provide important opportunities to accelerate the scientific process and further enhance its relevance and contribution to society. The key alternative is a structure that incorporates larger organizational units to tackle larger and more complex problems. One example of such a unit is the research network. Brazil has utilized such networks to great effect in genome sequencing projects, demonstrating their relevance to the Brazilian research community and opening the possibility of their wider utility in the future.
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Affiliation(s)
- Andrew J G Simpson
- Ludwig Institute for Cancer Research, 605 Third Avenue, New York, NY 10158, USA
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48
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Carraro DM, Camargo AA, Salim ACM, Gonzaga L, Costa GCD, Vasconcelos ATRD, Simpson AJG. Closure of rRNA related gaps in the Chromobacterium violaceum genome with the PCR-assisted contig extension (PACE) protocol. Genet Mol Res 2004; 3:53-63. [PMID: 15100987] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/29/2023]
Abstract
In the finishing phase of the Chromobacterium violaceum genome project, the shotgun sequences were assembled into 57 contigs that were then organized into 19 scaffolds, using the information from shotgun and cosmid clones. Among the 38 ends resulting from the 19 scaffolds, 10 ended with sequences corresponding to rRNA genes (seven ended with the 5S rRNA gene and three ended with the 16S rRNA gene). The 28 non-ribosomal ends were extended using the PCR-assisted contig extension (PACE) methodology, which immediately closed 15 real gaps. We then applied PACE to the 16S rRNA gene containing ends, resulting in eight different sequences that were correctly assembled within the C. violaceum genome by combinatory PCR strategy, with primers derived from the non-repetitive genomic region flanking the 16S and 5S rRNA gene. An oriented combinatory PCR was used to correctly position the two versions (copy A and copy B, which differ by the presence or absence of a 100-bp insert); it revealed six copies corresponding to copy A, and two to copy B. We estimate that the use of PACE, followed by combinatory PCR, accelerated the finishing phase of the C. violaceum genome project by at least 40%.
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Affiliation(s)
- Dirce Maria Carraro
- Laboratory of Genetics, Ludwig Institute for Cancer Research, São Paulo, SP, Brasil
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49
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Costa FF, Verbisck NV, Salim ACM, Ierardi DF, Pires LC, Sasahara RM, Sogayar MC, Zanata SM, Mackay A, O'Hare M, Soares F, Simpson AJG, Camargo AA. Epigenetic silencing of the adhesion molecule ADAM23 is highly frequent in breast tumors. Oncogene 2004; 23:1481-8. [PMID: 14661055 DOI: 10.1038/sj.onc.1207263] [Citation(s) in RCA: 48] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Altered cell adhesion is causally involved in tumor progression, and the identification of novel adhesion molecules altered in tumors is crucial for our understanding of tumor biology and for the development of new prognostic and therapeutic strategies. Here, we provide evidence for the epigenetic downregulation in breast tumors of the A Desintegrin And Metalloprotease domain 23 gene (ADAM 23), a member of a new family of surface molecules with roles in cell-cell adhesion and/or cell-matrix interactions. We examined the mRNA expression and methylation status of the 5' upstream region of the ADAM23 gene in different breast tumor cell lines as well as in primary breast tumors. We found ADAM23 5' hypermethylation in eight out of 12 (66.7%) tumor cell lines and in nine out of 13 (69.2%) primary tumors. Promoter hypermethylation was strongly associated with reductions in both mRNA and protein expression, with a threshold of 40-60% of modified CpG dinucleotides being required for the complete silencing of ADAM23 mRNA expression. Treatment of MCF-7 and SKBR-3 cell lines with 5'-Aza-2'-deoxycytidine led to a reactivation of ADAM23 mRNA expression and a marked decrease in the methylation level. It is worth noting that primary breast tumors with a more advanced grade showed a higher degree of methylation, suggesting that the adhesion molecule ADAM23 may be downregulated during the progression of breast cancer. Oncogene (2004) 23, 1481-1488. doi:10.1038/sj.onc.1207263 Published online 8 December 2003
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Affiliation(s)
- Fabrício F Costa
- Laboratory of Molecular Biology and Genomics, Ludwig Institute for Cancer Research, SP, Brazil
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50
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Vidigal THDA, Spatz L, Kissinger JC, Redondo RAF, Pires ECR, Simpson AJG, Carvalho OS. Analysis of the first and second internal transcribed spacer sequences of the ribosomal DNA in Biomphalaria tenagophila complex (Mollusca: Planorbidae). Mem Inst Oswaldo Cruz 2004; 99:153-8. [PMID: 15250468 DOI: 10.1590/s0074-02762004000200007] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The first and second internal transcribed spacer regions (ITS1 and ITS2) of the ribosomal DNA of Biomphalaria tenagophila complex (B. tenagophila, B. occidentalis, and B. t. guaibensis) were sequenced and compared. The alignment lengths of these regions were about 655 bp and 481 bp, respectively. Phylogenetic relationships among the Biomphalaria species were inferred by Maximum Parsimony and Neighbor-joining methods. The phylogenetic trees produced, in most of the cases, were in accordance with morphological systematics and other molecular data previously obtained by polymerase chain reaction and restriction fragment length polymorphism analysis. The present results provide support for the proposal that B. tenagophila represents a complex comprising B. tenagophila, B. occidentalis and B. t. guaibensis.
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Affiliation(s)
- Teofânia H D A Vidigal
- Centro de Pesquisas René Rachou-Fiocruz, Av. Augusto de Lima, 1715, 30190-002 Belo Horizonte, MG, Brasil
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