5701
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Teh MT, Tilakaratne WM, Chaplin T, Young BD, Ariyawardana A, Pitiyage G, Lalli A, Stewart JE, Hagi-Pavli E, Cruchley A, Waseem A, Fortune F. Fingerprinting genomic instability in oral submucous fibrosis. J Oral Pathol Med 2008; 37:430-6. [PMID: 18284545 DOI: 10.1111/j.1600-0714.2008.00643.x] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
BACKGROUND Oral submucous fibrosis (OSF) is a high-risk pre-cancerous condition where 7-13% of these patients develop head and neck squamous cell carcinoma (HNSCC). To date there is no cancer predictive markers for OSF patients. Genomic instability hallmarks early genetic events during malignant transformation causing loss of heterozygosity (LOH) and chromosomal copy number abnormality. However, to date there is no study on genomic instability in OSF. Although this condition is known as a high-risk pre-cancerous condition, there is no data regarding the genomic status of this disease in terms of genetic susceptibility to malignant transformation. METHODS In this study, we investigated the existence of genetic signatures for carcinogenesis in OSF. We employed the high-resolution genome-wide Affymetrix Mapping single nucleotide polymorphism microarray technique to 'fingerprint' global genomic instability in the form of LOH in 15 patient-matched OSF-blood genomic DNA samples. RESULTS This rapid high-resolution mapping technique has revealed for the first time that a small number of discrete hot-spot LOH loci appeared in 47-53% of the OSF tissues studied. Many of these LOH loci were previously identified regions of genomic instability associated with carcinogenesis of the HNSCC. CONCLUSION To our knowledge, this is the first evidence that genomic instability in the form of LOH is present in OSF. We hypothesize that the genomic instability detected in OSF may play an important role in malignant transformation. Further functional association studies on these putative genes may reveal potential predictive oral cancer markers for OSF patients.
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Affiliation(s)
- M T Teh
- Centre for Clinical and Diagnostic Oral Sciences, Barts and The London School of Medicine and Dentistry, Institute of Cell and Molecular Sciences Building, Queen Mary, University of London, London, UK
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5702
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Global survey of phosphotyrosine signaling identifies oncogenic kinases in lung cancer. Cell 2008; 131:1190-203. [PMID: 18083107 DOI: 10.1016/j.cell.2007.11.025] [Citation(s) in RCA: 1773] [Impact Index Per Article: 110.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2007] [Revised: 09/19/2007] [Accepted: 11/01/2007] [Indexed: 02/07/2023]
Abstract
Despite the success of tyrosine kinase-based cancer therapeutics, for most solid tumors the tyrosine kinases that drive disease remain unknown, limiting our ability to identify drug targets and predict response. Here we present the first large-scale survey of tyrosine kinase activity in lung cancer. Using a phosphoproteomic approach, we characterize tyrosine kinase signaling across 41 non-small cell lung cancer (NSCLC) cell lines and over 150 NSCLC tumors. Profiles of phosphotyrosine signaling are generated and analyzed to identify known oncogenic kinases such as EGFR and c-Met as well as novel ALK and ROS fusion proteins. Other activated tyrosine kinases such as PDGFRalpha and DDR1 not previously implicated in the genesis of NSCLC are also identified. By focusing on activated cell circuitry, the approach outlined here provides insight into cancer biology not available at the chromosomal and transcriptional levels and can be applied broadly across all human cancers.
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5703
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Ansari MI, Grohmann E, Malik A. Conjugative plasmids in multi-resistant bacterial isolates from Indian soil. J Appl Microbiol 2008; 104:1774-81. [PMID: 18284489 DOI: 10.1111/j.1365-2672.2008.03736.x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
AIMS Determination of heavy metal and antibiotic resistance and presence of conjugative plasmids in bacteria isolated from soil irrigated with wastewater. METHODS AND RESULTS Composite soil samples were collected from Ghaziabad, Uttar Pradesh, India. Forty different bacteria were selected from nutrient agar and characterized by morphological, cultural and biochemical tests. All the isolates were tested for their resistance to different heavy metals and antibiotics. The DNA derived from multiple metal and antibiotic-resistant bacterial isolates was PCR amplified and plasmid-specific sequences (IncP, IncN, IncW, IncQ and pMV158-type) were analysed by dot blot hybridization. All isolates gave PCR products with trfA2 and oriT primers of the IncP group. These PCR products also hybridized with the RP4-derived probes. However, the samples were negative for all the other investigated plasmids as proved by PCR and dot blots. CONCLUSIONS The presence of conjugative/mobilizable IncP plasmids in the isolates indicates that these bacteria have gene-mobilizing capacity with implications for potential dissemination of introduced recombinant DNA. SIGNIFICANCE AND IMPACT OF THE STUDY The detection of IncP plasmids in all the bacterial isolates is another proof for the prevalence of these plasmids. We propose that IncP plasmids are mainly responsible for the spread of multi-resistant bacteria in these soils.
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Affiliation(s)
- M I Ansari
- Department of Agricultural Microbiology, Faculty of Agricultural Sciences, Aligarh Muslim University, Aligarh, India
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5704
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Xu H, Yang L, Wang W, Shi SR, Liu C, Liu Y, Fang X, Taylor CR, Lee CS, Balgley BM. Antigen retrieval for proteomic characterization of formalin-fixed and paraffin-embedded tissues. J Proteome Res 2008; 7:1098-108. [PMID: 18257518 DOI: 10.1021/pr7006768] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Formalin-fixed and paraffin-embedded tissues represent the vast majority of archived tissue. Access to such tissue specimens via shotgun-based proteomic analyses may open new avenues for both prospective and retrospective translational research. In this study, we evaluate the effects of fixation time on antigen retrieval for the purposes of shotgun proteomics. For the first time, we demonstrate the capability of a capillary isotachophoresis (CITP)-based proteomic platform for the shotgun proteomic analysis of proteins recovered from FFPE tissues. In comparison to our previous studies utilizing capillary isoelectric focusing, the CITP-based analysis is more robust and increases proteome coverage. In this case, results from three FFPE liver tissues yield a total of 4098 distinct Swiss-Prot identifications at a 1% false-discovery rate. To judge the accuracy of these assignments, immunohistochemistry is performed on a panel of 17 commonly assayed proteins. These proteins span a wide range of protein abundances as inferred from relative quantitation via spectral counting. Among the panel were 4 proteins identified by a single peptide hit, including three clusters of differentiation (CD) markers: CD74, CD117, and CD45. Because single peptide hits are often regarded with skepticism, it is notable that all proteins tested by IHC stained positive.
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Affiliation(s)
- Haifeng Xu
- Calibrant Biosystems, 910 Clopper Road, Suite 220N, Gaithersburg, Maryland 20878, USA
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5705
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Haluska F, Pemberton T, Ibrahim N, Kalinsky K. The RTK/RAS/BRAF/PI3K pathways in melanoma: biology, small molecule inhibitors, and potential applications. Semin Oncol 2008; 34:546-54. [PMID: 18083378 DOI: 10.1053/j.seminoncol.2007.09.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The discovery of mutations in the BRAF signaling molecule in a large proportion of cutaneous melanomas immediately suggested the prospect of effective therapies for this disease. The most appealing initial target has been BRAF itself, as most mutations involve a single residue in the kinase domain of the protein. But the identification of the high mutation rate in this signaling intermediate also suggests that other molecules up- and downstream of BRAF might be productively targeted. Indeed, several receptor tyrosine kinases, as well as RAS, are mutated in a small number of melanoma cases. Moreover, genetic alterations in the phosphotidylinositol-3-kinase (PI3K) pathway, especially in PTEN, suggest that this route also poses opportunities for therapeutic exploitation. We will review here the genetic evidence suggesting the utility of targets on these pathways. We will also summarize the recent clinical data that have accumulated from initial trials designed to test BRAF inhibition and targeting of other molecules. Finally, we provide an overview of molecules entering the clinic and soon to be tested in clinical studies, as well as strategies for their employment as monotherapy and in combinations.
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Affiliation(s)
- Frank Haluska
- Molecular Oncology Research Institute, Tufts-New England Medical Center, Boston, MA 02111, USA.
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5706
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Lin WM, Baker AC, Beroukhim R, Winckler W, Feng W, Marmion JM, Laine E, Greulich H, Tseng H, Gates C, Hodi FS, Dranoff G, Sellers WR, Thomas RK, Meyerson M, Golub TR, Dummer R, Herlyn M, Getz G, Garraway LA. Modeling genomic diversity and tumor dependency in malignant melanoma. Cancer Res 2008; 68:664-73. [PMID: 18245465 PMCID: PMC10493008 DOI: 10.1158/0008-5472.can-07-2615] [Citation(s) in RCA: 245] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The classification of human tumors based on molecular criteria offers tremendous clinical potential; however, discerning critical and "druggable" effectors on a large scale will also require robust experimental models reflective of tumor genomic diversity. Here, we describe a comprehensive genomic analysis of 101 melanoma short-term cultures and cell lines. Using an analytic approach designed to enrich for putative "driver" events, we show that cultured melanoma cells encompass the spectrum of significant genomic alterations present in primary tumors. When annotated according to these lesions, melanomas cluster into subgroups suggestive of distinct oncogenic mechanisms. Integrating gene expression data suggests novel candidate effector genes linked to recurrent copy gains and losses, including both phosphatase and tensin homologue (PTEN)-dependent and PTEN-independent tumor suppressor mechanisms associated with chromosome 10 deletions. Finally, sample-matched pharmacologic data show that FGFR1 mutations and extracellular signal-regulated kinase (ERK) activation may modulate sensitivity to mitogen-activated protein kinase/ERK kinase inhibitors. Genetically defined cell culture collections therefore offer a rich framework for systematic functional studies in melanoma and other tumors.
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Affiliation(s)
- William M. Lin
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Alissa C. Baker
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
| | - Rameen Beroukhim
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Wendy Winckler
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Whei Feng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | | | - Elisabeth Laine
- Department of Dermatology, University of Zurich Hospital, Zürich, Switzerland
| | - Heidi Greulich
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Hsiuyi Tseng
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
| | | | - F. Stephen Hodi
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
| | - Glenn Dranoff
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
| | - William R. Sellers
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Novartis Institutes for Biomedical Research, Cambridge, Massachusetts
| | - Roman K. Thomas
- Max Planck Institute for Neurological Research with Klaus Joachim Zulch Laboratories of the Max Planck Society and the Medical Faculty of the University of Cologne
- Center for Integrated Oncology and Department I for Internal Medicine, University of Cologne, Cologne, Germany
| | - Matthew Meyerson
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Pathology, Harvard Medical School, Boston, Massachusetts
- The Broad Institute of M.I.T. and Harvard
| | - Todd R. Golub
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Reinhard Dummer
- Department of Dermatology, University of Zurich Hospital, Zürich, Switzerland
| | - Meenhard Herlyn
- Cancer Biology Division, Wistar Institute, Philadelphia, Pennsylvania
| | - Gad Getz
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
| | - Levi A. Garraway
- Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School
- Department of Center for Cancer Genome Discovery, Dana-Farber Cancer Institute, Harvard Medical School
- The Broad Institute of M.I.T. and Harvard
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5707
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Liakakos T, Roukos DH. More controversy than ever - challenges and promises towards personalized treatment of gastric cancer. Ann Surg Oncol 2008; 15:956-60. [PMID: 18214617 PMCID: PMC2266788 DOI: 10.1245/s10434-007-9798-5] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2007] [Accepted: 12/12/2007] [Indexed: 02/03/2023]
Affiliation(s)
- Theodore Liakakos
- Department of Surgery, Ioannina University School of Medicine, Ioannina University, GR-45110, Ioannina, 45, Greece
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5708
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Roukos DH. Innovative genomic-based model for personalized treatment of gastric cancer: integrating current standards and new technologies. Expert Rev Mol Diagn 2008; 8:29-39. [PMID: 18088228 DOI: 10.1586/14737159.8.1.29] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
In the era of network biology, understanding the complexity of the signaling pathways network in cancer origin, progression and metastasis will dramatically alter and improve treatment strategies. Prognosis of gastric cancer remains poor. Clinical decisions on treatment are based on tumor-node-metastasis (TNM) staging, but are suboptimal. This perspective review, integrating several concepts, including cancer stem cells, provides a novel treatment model for tailoring the best treatment in individual patients with gastric cancer. Biologic metastatic steps (invasion, angiogenesis, intra/extravasation, colonization and microenvironment at distant organs) are orchestrated by mutated genes. Identifying and profiling these key genes and their interactions with environmental factors such as Helicobacter pylori, driver mutations and interacting signaling pathways using high-throughput technologies (including omics, resequencing, genome-wide associations studies and RNAi) in unbiased studies can lead to the development of both novel biomarkers and targeted agents. A comprehensive bench-to-bedside treatment-guided algorithm is provided for optimum preoperative or postoperative combination of cytotoxic and targeted agents. The protocol can be applied with adequate modification for most solid tumors.
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Affiliation(s)
- Dimitrios H Roukos
- Surgical Oncology Research Unit, Department of Surgery, Ioannina University School of Medicine, GR 451 10 Ioannina, Greece.
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5709
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Camps M, Herman A, Loh E, Loeb LA. Genetic constraints on protein evolution. Crit Rev Biochem Mol Biol 2008; 42:313-26. [PMID: 17917869 DOI: 10.1080/10409230701597642] [Citation(s) in RCA: 90] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Evolution requires the generation and optimization of new traits ("adaptation") and involves the selection of mutations that improve cellular function. These mutations were assumed to arise by selection of neutral mutations present at all times in the population. Here we review recent evidence that indicates that deleterious mutations are more frequent in the population than previously recognized and that these mutations play a significant role in protein evolution through continuous positive selection. Positively selected mutations include adaptive mutations, i.e. mutations that directly affect enzymatic function, and compensatory mutations, which suppress the pleiotropic effects of adaptive mutations. Compensatory mutations are by far the most frequent of the two and would allow potentially adaptive but deleterious mutations to persist long enough in the population to be positively selected during episodes of adaptation. Compensatory mutations are, by definition, context-dependent and thus constrain the paths available for evolution. This provides a mechanistic basis for the examples of highly constrained evolutionary landscapes and parallel evolution reported in natural and experimental populations. The present review article describes these recent advances in the field of protein evolution and discusses their implications for understanding the genetic basis of disease and for protein engineering in vitro.
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Affiliation(s)
- Manel Camps
- Department of Environmental Toxicology, University of California at Santa Cruz, Santa Cruz, California 95064, USA.
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5710
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Abstract
The rhomboids are a well-conserved family of intramembrane serine proteases, which are unrelated to the classical soluble serine proteases. Their active site is buried within the plane of the membrane, and they cleave substrates in or near transmembrane domains. Although recently discovered, it is becoming clear that rhomboids control many important cellular functions. This review briefly describes recent biochemical and structural work that begins to explain how proteolysis occurs in a hydrophobic environment, but then focuses more extensively on the emerging biological functions of rhomboids. Although the function of most rhomboids is not yet known, they have already been implicated in growth factor signaling, mitochondrial function, host cell invasion by apicomplexan parasites, and protein translocation across membranes in bacteria. By exploiting cellular membrane trafficking machinery, rhomboids have evolved novel strategies to regulate proteolysis.
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5711
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Denley A, Gymnopoulos M, Hart JR, Jiang H, Zhao L, Vogt PK. Biochemical and biological characterization of tumor-associated mutations of p110alpha. Methods Enzymol 2008; 438:291-305. [PMID: 18413256 DOI: 10.1016/s0076-6879(07)38020-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Signaling by class I phosphatidylinositol 3-kinase (PI3K) controls cell growth, replication, motility, and metabolism. The PI3K pathway commonly shows gain of function in cancer. Two small GTPases, Rheb (Ras homolog enriched in brain) and Ras (rat sarcoma viral oncogene), play important roles in PI3K signaling. Rheb activates the TOR (target of rapamycin) kinase in a GTP-dependent manner; it links TOR to upstream signaling components, including the tuberous sclerosis complex (TSC) and Akt (homolog of the Akt8 murine lymphoma viral oncoprotein). Constitutively active, GTP-bound Rheb is oncogenic in cell culture, and activity that requires farnesylation. Ras activates PI3K by recruitment to the plasma membrane and possibly by inducing a conformational change in the catalytic subunit p110 of PI3K. In return, Ras signaling through the MAP kinase (MAPK) pathway is activated by PIP(3), the product of PI3K. Loss of Ras function can interfere with PI3K signaling. Various lines of evidence suggest complementary roles for PI3K and MAPK signaling in oncogenesis.
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Affiliation(s)
- Adam Denley
- Department of Molecular and Experimental Medicine, The Scripps Research Institute, La Jolla, California, USA
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5712
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Cui G, Zhang Y, Liu C, Skinner S, Qin Y. Pancreatic Cancer Suppression by Natural Polyphenols. ACTA ACUST UNITED AC 2008. [DOI: 10.3814/2008/540872] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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5713
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Abstract
Abstract
The difference between success and failure of treatment of acute myeloid leukemia (AML) is largely determined by genotypic leukemia-specific differences among patients. The diversity of AML genotypes result from somatic genetic alterations settling down in succession in an individual’s leukemia clone during the development of the disease. Gene mutations, gene expression abnormalities and other molecular alterations (e.g., microRNA variations) affect critical functions in AML cells, and may exert profound effects on the therapeutic response and outcome of the disease. Prototypes of common clinically significant gene aberrations involve transcription factors, signaling molecules and growth factor receptors. The expanding knowledge in this area allowing for risk stratified therapy decisions and the development of targeted drug therapy, is becoming an increasingly important part of the modern individualized clinical management of AML. This chapter highlights recent insights into the diagnostic, prognostic and therapeutic impact of chromosomal (e.g., the so-called monosomal karyotype) as well as particular genomic abnormalities, and presents examples of decision algorithms for individualized therapy.
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5714
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Abstract
A new generation of non-Sanger-based sequencing technologies has delivered on its promise of sequencing DNA at unprecedented speed, thereby enabling impressive scientific achievements and novel biological applications. However, before stepping into the limelight, next-generation sequencing had to overcome the inertia of a field that relied on Sanger-sequencing for 30 years.
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Affiliation(s)
- Stephan C Schuster
- Pennsylvania State University, Center for Comparative Genomics and Bioinformatics, 310 Wartik Building, University Park, Pennsylvania 16802, USA.
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5715
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Abstract
We conducted a comprehensive analysis of a manually curated human signaling network containing 1634 nodes and 5089 signaling regulatory relations by integrating cancer-associated genetically and epigenetically altered genes. We find that cancer mutated genes are enriched in positive signaling regulatory loops, whereas the cancer-associated methylated genes are enriched in negative signaling regulatory loops. We further characterized an overall picture of the cancer-signaling architectural and functional organization. From the network, we extracted an oncogene-signaling map, which contains 326 nodes, 892 links and the interconnections of mutated and methylated genes. The map can be decomposed into 12 topological regions or oncogene-signaling blocks, including a few ‘oncogene-signaling-dependent blocks' in which frequently used oncogene-signaling events are enriched. One such block, in which the genes are highly mutated and methylated, appears in most tumors and thus plays a central role in cancer signaling. Functional collaborations between two oncogene-signaling-dependent blocks occur in most tumors, although breast and lung tumors exhibit more complex collaborative patterns between multiple blocks than other cancer types. Benchmarking two data sets derived from systematic screening of mutations in tumors further reinforced our findings that, although the mutations are tremendously diverse and complex at the gene level, clear patterns of oncogene-signaling collaborations emerge recurrently at the network level. Finally, the mutated genes in the network could be used to discover novel cancer-associated genes and biomarkers.
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5716
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Abstract
The success of molecularly targeted agents (MTA) in the treatment of cancer has led to the investigation of their use in combination with other MTAs and with conventional chemotherapies. An overview of the MTAs that have emerged as Food and Drug Administration-approved drugs is presented, along with a framework for the consideration of how MTAs can best be combined to maximize therapeutic effect.
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Affiliation(s)
- Eunice L Kwak
- Massachusetts General Hospital Cancer Center, Boston, Massachusetts 02114, USA.
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5717
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Estep AL, Palmer C, McCormick F, Rauen KA. Mutation analysis of BRAF, MEK1 and MEK2 in 15 ovarian cancer cell lines: implications for therapy. PLoS One 2007; 2:e1279. [PMID: 18060073 PMCID: PMC2093994 DOI: 10.1371/journal.pone.0001279] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2007] [Accepted: 11/13/2007] [Indexed: 11/23/2022] Open
Abstract
Background Among gynecologic cancers, ovarian cancer is the second most common and has the highest death rate. Cancer is a genetic disorder and arises due to the accumulation of somatic mutations in critical genes. An understanding of the genetic basis of ovarian cancer has implications both for early detection and for therapeutic intervention in this population of patients. Methodology/Principal Findings Fifteen ovarian cancer cell lines, commonly used for in vitro experiments, were screened for mutations using bidirectional direct sequencing in all coding regions of BRAF, MEK1 and MEK2. BRAF mutations were identified in four of the fifteen ovarian cancer cell lines studied. Together, these four cell lines contained four different BRAF mutations, two of which were novel. ES-2 had the common B-Raf p.V600E mutation in exon 15 and Hey contained an exon 11 missense mutation, p.G464E. The two novel B-Raf mutants identified were a 5 amino acid heterozygous deletion p.N486-P490del in OV90, and an exon 4 missense substitution p.Q201H in OVCAR 10. One of the cell lines, ES-2, contained a mutation in MEK1, specifically, a novel heterozygous missense substitution, p.D67N which resulted from a nt 199 G→A transition. None of the cell lines contained coding region mutations in MEK2. Functional characterization of the MEK1 mutant p.D67N by transient transfection with subsequent Western blot analysis demonstrated increased ERK phosphorylation as compared to controls. Conclusions/Significance In this study, we report novel BRAF mutations in exon 4 and exon 12 and also report the first mutation in MEK1 associated with human cancer. Functional data indicate the MEK1 mutation may confer alteration of activation through the MAPK pathway. The significance of these findings is that BRAF and MEK1/2 mutations may be more common than anticipated in ovarian cancer which could have important implications for treatment of patients with this disease and suggests potential new therapeutic avenues.
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Affiliation(s)
- Anne L. Estep
- Comprehensive Cancer Center and Cancer Research Institute, University of California at San Francisco, San Francisco, California, United States of America
| | - Chana Palmer
- Canary Foundation, San Jose, California, United States of America
| | - Frank McCormick
- Comprehensive Cancer Center and Cancer Research Institute, University of California at San Francisco, San Francisco, California, United States of America
- Department of Microbiology and Immunology, University of California at San Francisco, San Francisco, California, United States of America
| | - Katherine A. Rauen
- Comprehensive Cancer Center and Cancer Research Institute, University of California at San Francisco, San Francisco, California, United States of America
- Department of Pediatrics, University of California at San Francisco, San Francisco, California, United States of America
- * To whom correspondence should be addressed. E-mail:
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5718
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Ruhe JE, Streit S, Hart S, Wong CH, Specht K, Knyazev P, Knyazeva T, Tay LS, Loo HL, Foo P, Wong W, Pok S, Lim SJ, Ong H, Luo M, Ho HK, Peng K, Lee TC, Bezler M, Mann C, Gaertner S, Hoefler H, Iacobelli S, Peter S, Tay A, Brenner S, Venkatesh B, Ullrich A. Genetic Alterations in the Tyrosine Kinase Transcriptome of Human Cancer Cell Lines. Cancer Res 2007; 67:11368-76. [DOI: 10.1158/0008-5472.can-07-2703] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5719
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Fröhling S, Scholl C, Levine RL, Loriaux M, Boggon TJ, Bernard OA, Berger R, Döhner H, Döhner K, Ebert BL, Teckie S, Golub TR, Jiang J, Schittenhelm MM, Lee BH, Griffin JD, Stone RM, Heinrich MC, Deininger MW, Druker BJ, Gilliland DG. Identification of driver and passenger mutations of FLT3 by high-throughput DNA sequence analysis and functional assessment of candidate alleles. Cancer Cell 2007; 12:501-13. [PMID: 18068628 DOI: 10.1016/j.ccr.2007.11.005] [Citation(s) in RCA: 152] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/03/2007] [Revised: 09/01/2007] [Accepted: 11/01/2007] [Indexed: 11/19/2022]
Abstract
Mutations in the juxtamembrane and kinase domains of FLT3 are common in AML, but it is not known whether alterations outside these regions contribute to leukemogenesis. We used a high-throughput platform to interrogate the entire FLT3 coding sequence in AML patients without known FLT3 mutations and experimentally tested the consequences of each candidate leukemogenic allele. This approach identified gain-of-function mutations that activated downstream signaling and conferred sensitivity to FLT3 inhibition and alleles that were not associated with kinase activation, including mutations in the catalytic domain. These findings support the concept that acquired mutations in cancer may not contribute to malignant transformation and underscore the importance of functional studies to distinguish "driver" mutations underlying tumorigenesis from biologically neutral "passenger" alterations.
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Affiliation(s)
- Stefan Fröhling
- Division of Hematology, Brigham and Women's Hospital, Harvard Medical School, Boston, MA 02115, USA
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5720
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Pujana MA, Han JDJ, Starita LM, Stevens KN, Tewari M, Ahn JS, Rennert G, Moreno V, Kirchhoff T, Gold B, Assmann V, Elshamy WM, Rual JF, Levine D, Rozek LS, Gelman RS, Gunsalus KC, Greenberg RA, Sobhian B, Bertin N, Venkatesan K, Ayivi-Guedehoussou N, Solé X, Hernández P, Lázaro C, Nathanson KL, Weber BL, Cusick ME, Hill DE, Offit K, Livingston DM, Gruber SB, Parvin JD, Vidal M. Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat Genet 2007; 39:1338-49. [PMID: 17922014 DOI: 10.1038/ng.2007.2] [Citation(s) in RCA: 424] [Impact Index Per Article: 24.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2007] [Accepted: 08/02/2007] [Indexed: 12/29/2022]
Abstract
Many cancer-associated genes remain to be identified to clarify the underlying molecular mechanisms of cancer susceptibility and progression. Better understanding is also required of how mutations in cancer genes affect their products in the context of complex cellular networks. Here we have used a network modeling strategy to identify genes potentially associated with higher risk of breast cancer. Starting with four known genes encoding tumor suppressors of breast cancer, we combined gene expression profiling with functional genomic and proteomic (or 'omic') data from various species to generate a network containing 118 genes linked by 866 potential functional associations. This network shows higher connectivity than expected by chance, suggesting that its components function in biologically related pathways. One of the components of the network is HMMR, encoding a centrosome subunit, for which we demonstrate previously unknown functional associations with the breast cancer-associated gene BRCA1. Two case-control studies of incident breast cancer indicate that the HMMR locus is associated with higher risk of breast cancer in humans. Our network modeling strategy should be useful for the discovery of additional cancer-associated genes.
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Affiliation(s)
- Miguel Angel Pujana
- Center for Cancer Systems Biology (CCSB), Dana-Farber Cancer Institute and Department of Genetics, Harvard Medical School, 44 Binney St., Boston, Massachusetts 02115, USA
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5721
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Lemberg MK, Freeman M. Functional and evolutionary implications of enhanced genomic analysis of rhomboid intramembrane proteases. Genes Dev 2007; 17:1634-46. [PMID: 17938163 PMCID: PMC2045146 DOI: 10.1101/gr.6425307] [Citation(s) in RCA: 175] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2007] [Accepted: 08/28/2007] [Indexed: 12/30/2022]
Abstract
Rhomboids are a recently discovered family of widely distributed intramembrane serine proteases. They have diverse biological functions, including the regulation of growth factor signaling, mitochondrial fusion, and parasite invasion. Despite their existence in all branches of life, the sequence identity between rhomboids is low. We have combined BLAST-based database mining with functional and structural data to generate a comprehensive genomic analysis of eukaryotic rhomboid-like proteins. We show that robust membrane topology models are necessary to classify active rhomboid proteases unambiguously, and we define rules for distinguishing predicted active proteases from the larger evolutionary group of rhomboid-like proteins. This leads to a revision of estimates of numbers of proteolytically active rhomboids. We identify three groups of eukaryotic rhomboid-like proteins: true active rhomboids, a tightly clustered group of novel inactive rhomboids that we name the iRhoms, and a small number of other inactive rhomboid-like proteins. The active proteases are themselves subdivided into secretase and PARL-type (mitochondrial) subfamilies; these have distinct transmembrane topologies. This enhanced genomic analysis leads to conclusions about rhomboid enzyme function. It suggests that a given rhomboid can only cleave a single orientation of substrate, and that both products of rhomboid catalyzed intramembrane cleavage can be released from the membrane. Our phylogeny predictions also have evolutionary implications: Despite the complex classification of rhomboids, our data suggest that a rhomboid-type intramembrane protease may have been present in the last eukaryotic common ancestor.
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Affiliation(s)
- Marius K. Lemberg
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
| | - Matthew Freeman
- MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
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5722
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Kanayama N, Takarada T, Kimura A, Shibata H, Maeda M. Poly(ethylene glycol)-oligodeoxyribonucleotide block copolymers for affinity capillary electrophoretic separation of single-stranded DNAs with a single-base difference. REACT FUNCT POLYM 2007. [DOI: 10.1016/j.reactfunctpolym.2007.07.036] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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5723
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Bennett DC. REVIEW ARTICLE: How to make a melanoma: what do we know of the primary clonal events? Pigment Cell Melanoma Res 2007; 21:27-38. [DOI: 10.1111/j.1755-148x.2007.00433.x] [Citation(s) in RCA: 149] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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5724
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Kato S, Iida S, Higuchi T, Ishikawa T, Takagi Y, Yasuno M, Enomoto M, Uetake H, Sugihara K. PIK3CA mutation is predictive of poor survival in patients with colorectal cancer. Int J Cancer 2007; 121:1771-8. [PMID: 17590872 DOI: 10.1002/ijc.22890] [Citation(s) in RCA: 113] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The PI3K-AKT pathway is activated in a variety of human cancers, resulting in disturbance of cell growth, proliferation and survival. Among the factors affecting the pathway, the K-Ras mutation and PIK3CA mutation are the most common oncogenic alterations in colorectal cancer. We hypothesized that these two mutations are important in activation of the PI3K pathway and colorectal carcinogenesis. In this study, we aimed to examine the influence of PIK3CA mutation and K-Ras mutation on AKT activation, and to clarify whether PIK3CA mutation, K-Ras mutation and p-AKT expression may be used as parameters for predicting prognosis in colorectal cancer. Tissue samples from 158 colorectal cancer patients who underwent surgical resection were examined. The sequences of exon 1 of K-Ras and exons 9 and 20 of PIK3CA were determined by direct sequencing using genomic DNA extracted from paraffin-embedded blocks. Activation status of AKT was evaluated by immunohistochemical staining using phospho-specific AKT antibody (Ser473). Correlation between these factors and clinicopathologic findings/patient survival were examined. As a result, PIK3CA mutation was significantly associated with shorter relapse-free survival (RFS) in stage II/III patients (p = 0.0216) and shorter disease-specific survival in all patients (p = 0.0357). In the multivariate analysis, PIK3CA mutation was the only independent and significant prognostic factor for RFS in stage II/III patients (p = 0.0433, HR 2.478). This study revealed the prognostic value of PIK3CA mutation in colorectal cancer patients. Patients with PIK3CA mutation should be followed up carefully. Moreover, our result suggests that inhibition of PIK3CA mutant may be a new molecular target therapy.
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Affiliation(s)
- Shunsuke Kato
- Department of Surgical Oncology, Graduate School, Tokyo Medical and Dental University, Tokyo, Japan.
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5725
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Wood LD, Parsons DW, Jones S, Lin J, Sjöblom T, Leary RJ, Shen D, Boca SM, Barber T, Ptak J, Silliman N, Szabo S, Dezso Z, Ustyanksky V, Nikolskaya T, Nikolsky Y, Karchin R, Wilson PA, Kaminker JS, Zhang Z, Croshaw R, Willis J, Dawson D, Shipitsin M, Willson JKV, Sukumar S, Polyak K, Park BH, Pethiyagoda CL, Pant PVK, Ballinger DG, Sparks AB, Hartigan J, Smith DR, Suh E, Papadopoulos N, Buckhaults P, Markowitz SD, Parmigiani G, Kinzler KW, Velculescu VE, Vogelstein B. The genomic landscapes of human breast and colorectal cancers. Science 2007; 318:1108-13. [PMID: 17932254 DOI: 10.1126/science.1145720] [Citation(s) in RCA: 2225] [Impact Index Per Article: 130.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
Human cancer is caused by the accumulation of mutations in oncogenes and tumor suppressor genes. To catalog the genetic changes that occur during tumorigenesis, we isolated DNA from 11 breast and 11 colorectal tumors and determined the sequences of the genes in the Reference Sequence database in these samples. Based on analysis of exons representing 20,857 transcripts from 18,191 genes, we conclude that the genomic landscapes of breast and colorectal cancers are composed of a handful of commonly mutated gene "mountains" and a much larger number of gene "hills" that are mutated at low frequency. We describe statistical and bioinformatic tools that may help identify mutations with a role in tumorigenesis. These results have implications for understanding the nature and heterogeneity of human cancers and for using personal genomics for tumor diagnosis and therapy.
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Affiliation(s)
- Laura D Wood
- Ludwig Center for Cancer Genetics and Therapeutics and Howard Hughes Medical Institute at Johns Hopkins Kimmel Cancer Center, Baltimore, MD 21231, USA
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5726
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Heaphy CM, Bisoffi M, Griffith JK. Diagnostic significance of allelic imbalance in cancer. EXPERT OPINION ON MEDICAL DIAGNOSTICS 2007; 1:159-68. [PMID: 23489303 DOI: 10.1517/17530059.1.2.159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Allelic imbalance (AI), a deviation from the normal 1:1 ratio of maternal and paternal alleles, occurs in virtually all solid and blood-borne malignancies. The frequency and spectrum of AI in a tumor cell reflects the karyotypic complexity of the cancer genome. Hence, many investigations have assessed the extent of AI to analyze differences between normal and tumor tissues in a variety of different organs. In this review, the authors describe established and emerging technologies used to assess the extent of AI in human tissues, and their application in the diagnosis of cancer. The four major methods to be reviewed represent powerful and widely used tools for the identification of allelic imbalances accompanying cancer initiation and progression. These are fluorescent in situ hybridization, comparative genomic hybridization, single nucleotide polymorphism arrays and the use of microsatellite markers. For each method, the authors provide a brief description of the approach and elaborate on specific studies that highlight its utility in the diagnosis of human cancers.
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Affiliation(s)
- Christopher M Heaphy
- Graduate Research Assistant, University of New Mexico School of Medicine, Department of Biochemistry and Molecular Biology, MSC08 4670, 1 University of New Mexico, Albuquerque, New Mexico 87131-0001, USA +1 505 272 5090 ; +1 505 272 6587 ;
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5727
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Beckmann JS, Estivill X, Antonarakis SE. Copy number variants and genetic traits: closer to the resolution of phenotypic to genotypic variability. Nat Rev Genet 2007; 8:639-46. [PMID: 17637735 DOI: 10.1038/nrg2149] [Citation(s) in RCA: 293] [Impact Index Per Article: 17.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
A considerable and unanticipated plasticity of the human genome, manifested as inter-individual copy number variation, has been discovered. These structural changes constitute a major source of inter-individual genetic variation that could explain variable penetrance of inherited (Mendelian and polygenic) diseases and variation in the phenotypic expression of aneuploidies and sporadic traits, and might represent a major factor in the aetiology of complex, multifactorial traits. For these reasons, an effort should be made to discover all common and rare copy number variants (CNVs) in the human population. This will also enable systematic exploration of both SNPs and CNVs in association studies to identify the genomic contributors to the common disorders and complex traits.
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Affiliation(s)
- Jacques S Beckmann
- Department of Medical Genetics, University of Lausanne and Centre Hospitalier Universitaire Vaudois, 2 Avenue Pierre Decker, 1011 Lausanne, Switzerland.
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5728
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Van Buskirk C, Sternberg PW. Epidermal growth factor signaling induces behavioral quiescence in Caenorhabditis elegans. Nat Neurosci 2007; 10:1300-7. [PMID: 17891142 DOI: 10.1038/nn1981] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/09/2007] [Accepted: 08/17/2007] [Indexed: 01/12/2023]
Abstract
The epidermal growth factor receptor (EGFR)/ErbB receptor tyrosine kinases regulate several aspects of development, including the development of the mammalian nervous system. ErbB signaling also has physiological effects on neuronal function, with influences on synaptic plasticity and daily cycles of activity. However, little is known about the effectors of EGFR activation in neurons. Here we show that EGF signaling has a nondevelopmental effect on behavior in Caenorhabditis elegans. Ectopic expression of the EGF-like ligand LIN-3 at any stage induces a reversible cessation of feeding and locomotion. These effects are mediated by neuronal EGFR (also called LET-23) and phospholipase C-gamma (PLC-gamma), diacylglycerol-binding proteins, and regulators of synaptic vesicle release. Activation of EGFR within a single neuron, ALA, is sufficient to induce a quiescent state. This pathway modulates the cessation of pharyngeal pumping and locomotion that normally occurs during the lethargus period that precedes larval molting. Our results reveal an evolutionarily conserved role for EGF signaling in the regulation of behavioral quiescence.
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Affiliation(s)
- Cheryl Van Buskirk
- Howard Hughes Medical Institute, Division of Biology 156-29, California Institute of Technology, 1200 E. California Blvd. Pasadena, California 91125, USA
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5729
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Pao W, Ladanyi M. Epidermal growth factor receptor mutation testing in lung cancer: searching for the ideal method. Clin Cancer Res 2007; 13:4954-5. [PMID: 17785543 DOI: 10.1158/1078-0432.ccr-07-1387] [Citation(s) in RCA: 166] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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5730
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Joshi VA, Kucherlapati R. Pharmacogenomics of lung cancer: with a view to address EGFR-targeted therapies. Pharmacogenomics 2007; 8:1211-20. [DOI: 10.2217/14622416.8.9.1211] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Epidermal growth factor receptor (EGFR)-targeted therapies have demonstrated variable success in treating individuals with non-small-cell lung cancer. Understanding the molecular mechanisms of response and resistance to this class of treatment has led to patient selection strategies that may improve outcomes. The second generation of EGFR-targeted therapies is now under clinical evaluation and may prove to be successful at circumventing a portion of primary or acquired resistance to first-generation tyrosine kinase inhibitors. These principles are generally applicable to the field of targeted therapy and predictive pharmacogenomics.
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Affiliation(s)
- Victoria A Joshi
- Harvard Medical School – Partners Healthcare Center for Genetics and Genomics, Department of Pathology, Massachusetts General Hospital, MA, USA
| | - Raju Kucherlapati
- Harvard Medical School – Partners Healthcare Center for Genetics and Genomics, Department of Pathology, Massachusetts General Hospital, MA, USA
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5731
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Ali MM, Su S, Filipe CDM, Pelton R, Li Y. Enzymatic manipulations of DNA oligonucleotides on microgel: towards development of DNA-microgel bioassays. Chem Commun (Camb) 2007:4459-61. [PMID: 17971955 DOI: 10.1039/b709817k] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that DNA oligonucleotides covalently coupled to colloidal microgel can be manipulated by T4 DNA ligase for DNA ligation and by Phi29 DNA polymerase for rolling circle amplification (RCA). We also show that the long single-stranded RCA product can generate intensive fluorescence upon hybridization with complementary fluorescent DNA probe. We believe DNA-microgel conjugates can be explored for the development of DNA based bioassays and biosensors.
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Affiliation(s)
- Md Monsur Ali
- Department of Biochemistry and Biomedical Sciences, McMaster University, 1200 Main St. W., Hamilton, ON, L8N 3Z5, Canada
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5732
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Ross CW, Ouillette PD, Saddler CM, Shedden KA, Malek SN. Comprehensive Analysis of Copy Number and Allele Status Identifies Multiple Chromosome Defects Underlying Follicular Lymphoma Pathogenesis. Clin Cancer Res 2007; 13:4777-85. [PMID: 17699855 DOI: 10.1158/1078-0432.ccr-07-0456] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
PURPOSE Follicular lymphoma (FL) constitutes the second most common non-Hodgkin's lymphoma in the Western world. The clinical course is variable and only in part explained by known tumor-intrinsic or -extrinsic factors. FL carries the hallmark chromosomal translocation t(14;18), deregulating the expression of Bcl-2, but this is not sufficient to explain either FL biology or clinical behavior. EXPERIMENTAL DESIGN We have employed high-density genomic profiling technology using the Affymetrix 50K-XbaI oligonucleotide single nucleotide polymorphism-chip platform to interrogate the genomes of 58 fluorescence-activated cell-sorted (FACS) FL specimens for chromosomal copy number changes and 46 specimens for loss of heterozygosity (LOH). RESULTS We report (a) previously unknown high-frequency copy-neutral LOH (uniparental disomy) in FL on chromosomes 1p (approximately 50%) and 6p (approximately 30%); (b) that del6q is complex, as reported, with at least two regions of minimal common loss at 6q13-15 and 6q23-24, and that in addition, approximately 8% of FL specimens contain a homozygous deletion at 6q23.3-24.1 that spans the negative NFkappaB regulator A20 and the p53 apoptosis effector PERP; (c) that combined analysis of chromosome 17p for LOH, copy number, and p53 mutations shows that most p53 mutations in FL do not involve del17p. Finally, we map high-frequency LOH with and without copy loss on chromosomes 9p, 10q, and 16p and genomic gains on 2p15-16 and 8q24.22-24.3. CONCLUSIONS This comprehensive description of the pathologic anatomy of the FL genome uncovers novel genetic lesions and should aid with identification of genes relevant to FL biology and clinical behavior.
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Affiliation(s)
- Charles W Ross
- Division of Hematology and Oncology, Department of Internal Medicine, University of Michigan, Ann Arbor, Michigan 48109-0936, USA
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5733
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Ruan Y, Ooi HS, Choo SW, Chiu KP, Zhao XD, Srinivasan K, Yao F, Choo CY, Liu J, Ariyaratne P, Bin WG, Kuznetsov VA, Shahab A, Sung WK, Bourque G, Palanisamy N, Wei CL. Fusion transcripts and transcribed retrotransposed loci discovered through comprehensive transcriptome analysis using Paired-End diTags (PETs). Genome Res 2007; 17:828-38. [PMID: 17568001 PMCID: PMC1891342 DOI: 10.1101/gr.6018607] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Identification of unconventional functional features such as fusion transcripts is a challenging task in the effort to annotate all functional DNA elements in the human genome. Paired-End diTag (PET) analysis possesses a unique capability to accurately and efficiently characterize the two ends of DNA fragments, which may have either normal or unusual compositions. This unique nature of PET analysis makes it an ideal tool for uncovering unconventional features residing in the human genome. Using the PET approach for comprehensive transcriptome analysis, we were able to identify fusion transcripts derived from genome rearrangements and actively expressed retrotransposed pseudogenes, which would be difficult to capture by other means. Here, we demonstrate this unique capability through the analysis of 865,000 individual transcripts in two types of cancer cells. In addition to the characterization of a large number of differentially expressed alternative 5' and 3' transcript variants and novel transcriptional units, we identified 70 fusion transcript candidates in this study. One was validated as the product of a fusion gene between BCAS4 and BCAS3 resulting from an amplification followed by a translocation event between the two loci, chr20q13 and chr17q23. Through an examination of PETs that mapped to multiple genomic locations, we identified 4055 retrotransposed loci in the human genome, of which at least three were found to be transcriptionally active. The PET mapping strategy presented here promises to be a useful tool in annotating the human genome, especially aberrations in human cancer genomes.
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Affiliation(s)
- Yijun Ruan
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
- Corresponding authors.E-mail ; fax 65-64789059.E-mail ; fax 65-64789059
| | - Hong Sain Ooi
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Siew Woh Choo
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Kuo Ping Chiu
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Xiao Dong Zhao
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - K.G. Srinivasan
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Fei Yao
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Chiou Yu Choo
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Jun Liu
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Pramila Ariyaratne
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Wilson G.W. Bin
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Vladimir A. Kuznetsov
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | - Atif Shahab
- Bioinformatics Institute, Singapore 138671, Singapore
| | - Wing-Kin Sung
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
- School of Computing, National University of Singapore, Singapore 117543, Singapore
| | - Guillaume Bourque
- Information and Mathematical Science Group, Genome Institute of Singapore, Singapore 138672, Singapore
| | | | - Chia-Lin Wei
- Genome Technology and Biology Group, Genome Institute of Singapore, Singapore 138672, Singapore
- Corresponding authors.E-mail ; fax 65-64789059.E-mail ; fax 65-64789059
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5734
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5735
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Gottlieb B, Beitel LK, Trifiro M. Will knowledge of human genome variation result in changing cancer paradigms? Bioessays 2007; 29:678-85. [PMID: 17563087 DOI: 10.1002/bies.20595] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
Our incomplete understanding of carcinogenesis may be a significant reason why some cancer mortality rates are still increasing. This lack of understanding is likely due to a research approach that relies heavily on genetic comparison between cancerous and non-cancerous tissues and cells, which has led to the identification of genes of cancer proliferation rather than differentiation. Recent observations showing that a tremendous degree of natural human genetic variation occurs are likely to lead to a shift in the basic paradigms of cancer genetics, in that there is a need to consider both the nature of the genes involved, and the idea that not every genetic variation identified in these genes may be associated with carcinogenesis. Based on studies using LCM and micro-genetic analyses, we propose that significant cancer initiating events may take place during the very early stages of development of cancer-susceptible tissues and that using such techniques might greatly help us in our understanding of carcinogenesis.
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Affiliation(s)
- Bruce Gottlieb
- Lady Davis Institute for Medical Research, Sir Mortimer B. Davis-Jewish General Hospital, Montreal, Quebec, Canada.
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5736
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Mir MM, Dar JA, Dar NA, Syed AT, Salam I, Lone GN. The Association of Beta-catenin Gene Mutations and Human Papillomavirus in Carcinoma of Esophagus in a High-Risk Population of India. Int J Health Sci (Qassim) 2007; 1:177-183. [PMID: 21475426 PMCID: PMC3068640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/30/2023] Open
Abstract
BACKGROUND Esophageal cancer (EC) is the sixth leading cause of death from cancer. In high-risk regions, squamous cell carcinoma is the most common type of EC, and its etiology remains poorly understood. It shows uneven geographical distribution in its occurrence, reflecting the influence of local environmental conditions, lifestyle and genetic predisposition in the development of the cancer. Kashmir, in the north of India, has been described as a high-risk area for esophageal squamous cell carcinoma (ESCC). In the present investigation an attempt was made to study the role of β-catenin mutations and human papillomavirus in 62 ESCC patients from Kashmir. METHODS The hot spot mutation region of β-catenin exon 3 was evaluated in matched tumor and normal tissues using a combination of PCR-SSCP and direct sequencing. We used two different sets of consensus primers viz., GP5+ and GP6+; PGMY09 and PGMY11 in conjunction with reverse line blot assay to screen for human papillomavirus(HPV). RESULTS None of the tumors showed the presence of commonly reported mutations in β-catenin. In view of the fact that HPV has been linked to pathogenesis of EC, we screened all the tumor and control specimens for the presence of HPV and we didn't detect HPV in any of the matched tumor and control specimens in contrast to the positive controls we used. CONCLUSION In conclusion our results suggest that squamous cell carcinoma of esophagus in Kashmir may arise independent of oncogenic β-catenin mutations and HPV is unlikely to be an etiologic factor for ESCC in this region.
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Affiliation(s)
| | | | - Nazir Ahmad Dar
- Departments of Clinical Biochemistry
- P G Department of Biochemistry, University of Kashmir, Srinagar
| | | | | | - Ghulam Nabi Lone
- Cardiovascular thoracic surgery, Sheri-i- Kashmir Institute of Medical Sciences, Srinagar
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5737
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5738
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5739
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Chattopadhyay I, Kapur S, Purkayastha J, Phukan R, Kataki A, Mahanta J, Saxena S. Gene expression profile of esophageal cancer in North East India by cDNA microarray analysis. World J Gastroenterol 2007; 13:1438-44. [PMID: 17457978 PMCID: PMC4146931 DOI: 10.3748/wjg.v13.i9.1438] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 11/17/2006] [Revised: 12/29/2006] [Accepted: 01/26/2007] [Indexed: 02/07/2023] Open
Abstract
AIM To identify alterations in genes and molecular functional pathways in esophageal cancer in a high incidence region of India where there is a widespread use of tobacco and betel quid with fermented areca nuts. METHODS Total RNA was isolated from tumor and matched normal tissue of 16 patients with esophageal squamous cell carcinoma. Pooled tumor tissue RNA was labeled with Cy3-dUTP and pooled normal tissue RNA was labeled with Cy5-dUTP by direct labeling method. The labeled probes were hybridized with human 10K cDNA chip and expression profiles were analyzed by Genespring GX V 7.3 (Silicon Genetics). RESULTS Nine hundred twenty three genes were differentially expressed. Of these, 611 genes were upregulated and 312 genes were downregulated. Using stringent criteria (P < or = 0.05 and > or = 1.5 fold change), 127 differentially expressed genes (87 upregulated and 40 downregulated) were identified in tumor tissue. On the basis of Gene Ontology, four different molecular functional pathways (MAPK pathway, G-protein coupled receptor family, ion transport activity, and serine or threonine kinase activity) were most significantly upregulated and six different molecular functional pathways (structural constituent of ribosome, endopeptidase inhibitor activity, structural constituent of cytoskeleton, antioxidant activity, acyl group transferase activity, eukaryotic translation elongation factor activity) were most significantly downregulated. CONCLUSION Several genes that showed alterations in our study have also been reported from a high incidence area of esophageal cancer in China. This indicates that molecular profiles of esophageal cancer in these two different geographic locations are highly consistent.
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Affiliation(s)
- Indranil Chattopadhyay
- Institute of Pathology, Indian Council of Medical Research, Safdarjang Hospital Campus, Post Box No. 4909, New Delhi 110029, India
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5740
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Ma Y, Fiering S, Black C, Liu X, Yuan Z, Memoli VA, Robbins DJ, Bentley HA, Tsongalis GJ, Demidenko E, Freemantle SJ, Dmitrovsky E. Transgenic cyclin E triggers dysplasia and multiple pulmonary adenocarcinomas. Proc Natl Acad Sci U S A 2007; 104:4089-94. [PMID: 17360482 PMCID: PMC1820713 DOI: 10.1073/pnas.0606537104] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Cyclin E is a critical G(1)-S cell cycle regulator aberrantly expressed in bronchial premalignancy and lung cancer. Cyclin E expression negatively affects lung cancer prognosis. Its role in lung carcinogenesis was explored. Retroviral cyclin E transduction promoted pulmonary epithelial cell growth, and small interfering RNA targeting of cyclin E repressed this growth. Murine transgenic lines were engineered to mimic aberrant cyclin E expression in the lung. Wild-type and proteasome degradation-resistant human cyclin E transgenic lines were independently driven by the human surfactant C (SP-C) promoter. Chromosome instability (CIN), pulmonary dysplasia, sonic hedgehog (Shh) pathway activation, adenocarcinomas, and metastases occurred. Notably, high expression of degradation-resistant cyclin E frequently caused dysplasia and multiple lung adenocarcinomas. Thus, recapitulation of aberrant cyclin E expression as seen in human premalignant and malignant lung lesions reproduces in the mouse frequent features of lung carcinogenesis, including CIN, Shh pathway activation, dysplasia, single or multiple lung cancers, or presence of metastases. This article reports unique mouse lung cancer models that replicate many carcinogenic changes found in patients. These models provide insights into the carcinogenesis process and implicate cyclin E as a therapeutic target in the lung.
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Affiliation(s)
- Yan Ma
- Departments of *Pharmacology and Toxicology
| | - Steven Fiering
- Microbiology and Immunology
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755 and Dartmouth–Hitchcock Medical Center, Lebanon, NH 03756
| | - Candice Black
- Pathology, and
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755 and Dartmouth–Hitchcock Medical Center, Lebanon, NH 03756
| | - Xi Liu
- Departments of *Pharmacology and Toxicology
| | | | - Vincent A. Memoli
- Pathology, and
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755 and Dartmouth–Hitchcock Medical Center, Lebanon, NH 03756
| | - David J. Robbins
- Departments of *Pharmacology and Toxicology
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755 and Dartmouth–Hitchcock Medical Center, Lebanon, NH 03756
| | | | - Gregory J. Tsongalis
- Pathology, and
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755 and Dartmouth–Hitchcock Medical Center, Lebanon, NH 03756
| | - Eugene Demidenko
- Pathology, and
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755 and Dartmouth–Hitchcock Medical Center, Lebanon, NH 03756
| | | | - Ethan Dmitrovsky
- Departments of *Pharmacology and Toxicology
- Medicine
- Norris Cotton Cancer Center, Dartmouth Medical School, Hanover, NH 03755 and Dartmouth–Hitchcock Medical Center, Lebanon, NH 03756
- **To whom correspondence should be addressed. E-mail:
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5741
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Effects of dietary flavonoids on apoptotic pathways related to cancer chemoprevention. J Nutr Biochem 2007; 18:427-42. [PMID: 17321735 DOI: 10.1016/j.jnutbio.2006.11.004] [Citation(s) in RCA: 369] [Impact Index Per Article: 21.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2006] [Revised: 11/06/2006] [Accepted: 11/13/2006] [Indexed: 12/12/2022]
Abstract
Epidemiological studies have described the beneficial effects of dietary polyphenols (flavonoids) on the reduction of the risk of chronic diseases, including cancer. Moreover, it has been shown that flavonoids, such as quercetin in apples, epigallocatechin-3-gallate in green tea and genistein in soya, induce apoptosis. This programmed cell death plays a critical role in physiological functions, but there is underlying dysregulation of apoptosis in numerous pathological situations such as Parkinson's disease, Alzheimer's disease and cancer. At the molecular level, flavonoids have been reported to modulate a number of key elements in cellular signal transduction pathways linked to the apoptotic process (caspases and bcl-2 genes), but that regulation and induction of apoptosis are unclear. The aim of this review is to provide insights into the molecular basis of the potential chemopreventive activities of representative flavonoids, with emphasis on their ability to control intracellular signaling cascades responsible for regulating apoptosis, a relevant target in cancer-preventive approach.
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5742
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Bertolani C, Sancho-Bru P, Failli P, Bataller R, Aleffi S, DeFranco R, Mazzinghi B, Romagnani P, Milani S, Ginés P, Colmenero J, Parola M, Gelmini S, Tarquini R, Laffi G, Pinzani M, Marra F. Resistin as an intrahepatic cytokine: overexpression during chronic injury and induction of proinflammatory actions in hepatic stellate cells. THE AMERICAN JOURNAL OF PATHOLOGY 2007. [PMID: 17148667 DOI: 10.2353/ajpath] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
Obesity and insulin resistance accelerate the progression of fibrosis during chronic liver disease. Resistin antagonizes insulin action in rodents, but its role in humans is still controversial. The aims of this study were to investigate resistin expression in human liver and to evaluate whether resistin may affect the biology of activated human hepatic stellate cells (HSCs), key modulators of hepatic fibrogenesis. Resistin gene expression was low in normal human liver but was increased in conditions of severe fibrosis. Up-regulation of resistin during chronic liver damage was confirmed by immunohistochemistry. In a group of patients with alcoholic hepatitis, resistin expression correlated with inflammation and fibrosis, suggesting a possible action on HSCs. Exposure of cultured HSCs to recombinant resistin resulted in increased expression of the proinflammatory chemokines monocyte chemoattractant protein-1 and interleukin-8, through activation of nuclear factor (NF)-kappaB. Resistin induced a rapid increase in intracellular calcium concentration, mainly through calcium release from intracellular inositol triphosphate-sensitive pools. The intracellular calcium chelator BAPTA-AM blocked resistin-induced NF-kappaB activation and monocyte chemoattractant protein-1 expression. In conclusion, this study shows a role for resistin as an intrahepatic cytokine exerting proinflammatory actions in HSCs, via a Ca2+/NF-kappaB-dependent pathway and suggests involvement of this adipokine in the pathophysiology of liver fibrosis.
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Affiliation(s)
- Cristiana Bertolani
- Dipartimento di Medicina Interna, University of Florence, Viale Morgagni, 85, I-50134 Florence, Italy, and the Liver Unit, Hospital Clinic, Institut d'Investigacions Biomediques August Pi i Sunyer, Barcelona, Spain
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5743
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Abstract
The rhomboid gene was discovered in Drosophila, where it encodes a seven transmembrane protein that is the signal-generating component of epidermal growth factor (EGF) receptor signaling during development. Although metazoan developmental regulators are rarely conserved outside the animal kingdom, rhomboid proteins are conserved in all kingdoms of life, but the significance of this remains unclear. Recent biochemical reconstitution and high-resolution crystal structures have provided proof that rhomboid proteins function as novel intramembrane proteases, with a serine protease-like catalytic apparatus embedded within the membrane bilayer, buried in a hydrophilic cavity formed by a protein ring. A thorough consideration of all known examples of rhomboid function suggests that, despite biochemical similarity in mechanism and specificity, rhomboid proteins function in diverse processes including quorum sensing in bacteria, mitochondrial membrane fusion, apoptosis, and stem cell differentiation in eukaryotes; rhomboid proteins are also now starting to be linked to human disease, including early-onset blindness, diabetes, and parasitic diseases. Regulating cell signaling is at the heart of rhomboid protein function in many, but not all, of these processes. Further study of these novel enzymes promises to reveal the evolutionary path of rhomboid protein function, which could provide insights into the forces that drive the molecular evolution of regulatory mechanisms.
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Affiliation(s)
- Sinisa Urban
- Department of Molecular Biology and Genetics, Johns Hopkins University School of Medicine, Baltimore, Maryland 21205, USA.
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5744
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Gonzalez-Serricchio AS, Sternberg PW. Visualization of C. elegans transgenic arrays by GFP. BMC Genet 2006; 7:36. [PMID: 16759392 PMCID: PMC1539001 DOI: 10.1186/1471-2156-7-36] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2006] [Accepted: 06/07/2006] [Indexed: 11/15/2022] Open
Abstract
Background Targeting the green fluorescent protein (GFP) via the E. coli lac repressor (LacI) to a specific DNA sequence, the lac operator (lacO), allows visualization of chromosomes in yeast and mammalian cells. In principle this method of visualization could be used for genetic mosaic analysis, which requires cell-autonomous markers that can be scored easily and at single cell resolution. The C. elegans lin-3 gene encodes an epidermal growth factor family (EGF) growth factor. lin-3 is expressed in the gonadal anchor cell and acts through LET-23 (transmembrane protein tyrosine kinase and ortholog of EGF receptor) to signal the vulval precursor cells to generate vulval tissue. lin-3 is expressed in the vulval cells later, and recent evidence raises the possibility that lin-3 acts in the vulval cells as a relay signal during vulval induction. It is thus of interest to test the site of action of lin-3 by mosaic analysis. Results We visualized transgenes in living C. elegans by targeting the green fluorescent protein (GFP) via the E. coli lac repressor (LacI) to a specific 256 sequence repeat of the lac operator (lacO) incorporated into transgenes. We engineered animals to express a nuclear-localized GFP-LacI fusion protein. C. elegans cells having a lacO transgene result in nuclear-localized bright spots (i.e., GFP-LacI bound to lacO). Cells with diffuse nuclear fluorescence correspond to unbound nuclear localized GFP-LacI. We detected chromosomes in living animals by chromosomally integrating the array of the lacO repeat sequence and visualizing the integrated transgene with GFP-LacI. This detection system can be applied to determine polyploidy as well as investigating chromosome segregation. To assess the GFP-LacI•lacO system as a marker for mosaic analysis, we conducted genetic mosaic analysis of the epidermal growth factor lin-3, expressed in the anchor cell. We establish that lin-3 acts in the anchor cell to induce vulva development, demonstrating this method's utility in detecting the presence of a transgene. Conclusion The GFP-LacI•lacO transgene detection system works in C. elegans for visualization of chromosomes and extrachromosomal transgenes. It can be used as a marker for genetic mosaic analysis. The lacO repeat sequence as an extrachromosomal array becomes a valuable technique allowing rapid, accurate determination of spontaneous loss of the array, thereby allowing high-resolution mosaic analysis. The lin-3 gene is required in the anchor cell to induce the epidermal vulval precursors cells to undergo vulval development.
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Affiliation(s)
- Aidyl S Gonzalez-Serricchio
- Department of Biological Sciences, California State Polytechnic University, 3801 W Temple Avenue, Pomona, CA 91768, USA
| | - Paul W Sternberg
- Division of Biology and Howard Hughes Medical Institute, mail code 156-29, Caltech, Pasadena, CA 91125, USA
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5745
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Stetak A, Hoier EF, Croce A, Cassata G, Di Fiore PP, Hajnal A. Cell fate-specific regulation of EGF receptor trafficking during Caenorhabditis elegans vulval development. EMBO J 2006; 25:2347-57. [PMID: 16688213 PMCID: PMC1478196 DOI: 10.1038/sj.emboj.7601137] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2005] [Accepted: 04/18/2006] [Indexed: 11/08/2022] Open
Abstract
By controlling the subcellular localization of growth factor receptors, cells can modulate the activity of intracellular signal transduction pathways. During Caenorhabditis elegans vulval development, a ternary complex consisting of the LIN-7, LIN-2 and LIN-10 PDZ domain proteins localizes the epidermal growth factor receptor (EGFR) to the basolateral compartment of the vulval precursor cells (VPCs) to allow efficient receptor activation by the inductive EGF signal from the anchor cell. We have identified EGFR substrate protein-8 (EPS-8) as a novel component of the EGFR localization complex that links receptor trafficking to cell fate specification. EPS-8 expression is upregulated in the primary VPCs, where it creates a positive feedback loop in the EGFR/RAS/MAPK pathway. The membrane-associated guanylate kinase LIN-2 recruits EPS-8 into the receptor localization complex to retain the EGFR on the basolateral plasma membrane, and thus allow maximal receptor activation in the primary cell lineage. Low levels of EPS-8 in the neighboring secondary VPCs result in the rapid degradation of the EGFR, allowing these cells to adopt the secondary cell fate. Extracellular signals thus regulate EGFR trafficking in a cell type-specific manner to control pattern formation during organogenesis.
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Affiliation(s)
- Attila Stetak
- Institute of Zoology, University of Zürich, Zürich, Switzerland
| | | | - Assunta Croce
- IFOM-FIRC Institute of Molecular Oncology, Milano, Italy
| | | | | | - Alex Hajnal
- Institute of Zoology, University of Zürich, Zürich, Switzerland
- Institute of Zoology, University of Zürich, Winterthurerstr. 190, 8057 Zürich, Switzerland. Tel.: +41 1 635 4854/4866; Fax: +41 1 635 6878; E-mail:
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5746
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Cui M, Chen J, Myers TR, Hwang BJ, Sternberg PW, Greenwald I, Han M. SynMuv Genes Redundantly Inhibit lin-3/EGF Expression to Prevent Inappropriate Vulval Induction in C. elegans. Dev Cell 2006; 10:667-72. [PMID: 16678779 DOI: 10.1016/j.devcel.2006.04.001] [Citation(s) in RCA: 88] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2006] [Revised: 03/17/2006] [Accepted: 04/03/2006] [Indexed: 01/08/2023]
Abstract
Activation of EGFR-Ras-MAPK signaling in vulval precursor cells (VPCs) by LIN-3/EGF from the gonad induces vulval development in C. elegans. The prevailing view is that LIN-3 overcomes an "inhibitory signal" from the adjacent hyp7 hypodermal syncytium. This view originated from observations indicating that inactivation of functionally redundant Synthetic Multivulva (SynMuv) genes in hyp7 can activate EGFR-Ras-MAPK signaling in the VPCs. Many SynMuv genes encode transcription and chromatin-associated factors, including the Rb ortholog. Here, we show that the SynMuv A and SynMuv B gene classes are functionally redundant for transcriptional repression of the key target gene, lin-3/EGF, in the hypodermis. These observations necessitate a revision of the concept of "inhibitory signaling." They also underscore the importance of preventing inappropriate cell signaling during development and suggest that derepression of growth factors may be the mechanism by which tumor suppressor genes such as Rb can have cell nonautonomous effects.
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Affiliation(s)
- Mingxue Cui
- Howard Hughes Medical Institute, Department of MCD Biology, University of Colorado, Boulder, Colorado 80309, USA
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5747
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Canevascini S, Marti M, Fröhli E, Hajnal A. The Caenorhabditis elegans homologue of the proto-oncogene ect-2 positively regulates RAS signalling during vulval development. EMBO Rep 2006; 6:1169-75. [PMID: 16270101 PMCID: PMC1369209 DOI: 10.1038/sj.embor.7400574] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2005] [Revised: 09/22/2005] [Accepted: 10/10/2005] [Indexed: 11/08/2022] Open
Abstract
Guanine nucleotide exchange factors (GEFs) regulate the activity of small GTP-binding proteins in a variety of biological processes. We have identified a gain-of-function mutation in the Caenorhabditis elegans GEF ect-2, the homologue of the mammalian ect2 proto-oncogene that has an essential role during cytokinesis. Here, we report that, in addition to its known function during mitosis, ECT-2 promotes the specification of the primary vulval cell fate by activating RAS/mitogen-activated protein kinase (MAPK) signalling before the end of the S-phase. Epistasis analysis indicates that ECT-2 crosstalks to the canonical RAS/MAPK cascade upstream of the RAS GEF SOS-1 by means of a RHO-1 signalling pathway. Our results raise the possibility that the transforming activity of the mammalian ect-2 oncogene could be due to hyperactivation of the RAS/MAPK pathway.
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Affiliation(s)
- Stefano Canevascini
- Institute of Zoology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Mark Marti
- Institute of Zoology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Erika Fröhli
- Institute of Zoology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
| | - Alex Hajnal
- Institute of Zoology, University of Zürich, Winterthurerstrasse 190, 8057 Zürich, Switzerland
- Tel: +41 44 6354854; Fax: +41 44 6356878; E-mail:
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5748
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Murtaza I, Dutt A, Mushtaq D, Ali A. Molecular cloning and genetic analysis of functional merB gene from indian isolates of Escherichia coli. Curr Microbiol 2005; 51:297-302. [PMID: 16211434 DOI: 10.1007/s00284-005-0013-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2005] [Accepted: 05/30/2005] [Indexed: 02/08/2023]
Abstract
Studies were carried out to characterize organomercurial lyase genes from wild type mercury-resistant Escherichia coli isolates, previously collected from five geographically distinct regions of the Indian subcontinent. PCR amplification followed by DNA sequencing of amplified fragments showed three merB identical to the previously characterized mer B from E. coli pR831b that were thus considered as the same gene. The remaining two genes derived from E. coli isolates of an almost mercury-free site (Dal lake, Kashmir) and designated as pIAAD3 merB and pIAAD14 merB showed slight variation (2%) at base. However, this variation in pIAAD3 due to the absence of base "T" at 479 position results in complete frame shift and the predicted MerB-like polypeptide derived from it showed 21.53% divergent at its C terminal end from the previously characterized pR831b MerB. The expression profile of pIAAD3 merB in pQE30 and pUC18 vectors each demonstrated 22.2 kDa proteins. The induced DH5alpha E. coli cells possessing pIAAD3 merB cloned in pUC18 vector split phenyl mercuric acetate (PMA) into benzene and inorganic mercury efficiently, thus giving a clue that the expressed gene product is biologically active. The current study suggests that such genetic changes may take place in the continued absence of mercury pressure, and with such modifications, they finally break down to act as vestigial remnants. Further work is going on in our lab to exploit pIAAD3 merB for the bioremediation of mercury-polluted sites.
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Affiliation(s)
- Imtiyaz Murtaza
- Molecular Biotechnology and Biochemistry Laboratory, Division of PHT, S.K University of Agricultural Sciences and Technology of Kashmir, Shalimar Campus, Srinagar, Kashmir, India.
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5749
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Berset TA, Hoier EF, Hajnal A. The C. elegans homolog of the mammalian tumor suppressor Dep-1/Scc1 inhibits EGFR signaling to regulate binary cell fate decisions. Genes Dev 2005; 19:1328-40. [PMID: 15901674 PMCID: PMC1142556 DOI: 10.1101/gad.333505] [Citation(s) in RCA: 74] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
Protein phosphorylation by kinases and the subsequent dephosphorylation by phosphatases are key mechanisms that regulate intracellular signal transduction during development. Here, we report the identification of the receptor protein tyrosine phosphatase DEP-1 as a negative regulator of the Caenorhabditis elegans EGF receptor. DEP-1 amplifies in the developing vulva and the excretory system the small differences in the amount of EGF signal received by equivalent precursor cells to achieve binary cell fate decisions. During vulval development, DEP-1 inhibits EGFR signaling in the secondary cell lineage in parallel with the NOTCH-mediated lateral inhibition, while EGFR signaling simultaneously down-regulates DEP-1 and NOTCH expression in the primary cell lineage. This regulatory network of inhibitors results in the full activation of the EGFR/RAS/MAPK pathway in the primary vulval cells and at the same time keeps the EGFR/RAS/MAPK pathway inactive in the adjacent secondary cells. Mammalian Dep-1/Scc1 functions as a tumor-suppressor gene in the intestinal epithelium. Thus, mutations in human Dep-1 may promote tumor formation through a hyperactivation of the EGF receptor.
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5750
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Abstract
During a period of 16 years, 203 proven pancreatic ductal adenocarcinomas were studied. Tumor size was measured on either the resected or the autopsy specimen. Four tumors were smaller than 1 cm, and 17 tumors were between 1.1 and 2 cm. ERCP has been found to be the most accurate in the diagnosis of small pancreatic carcinoma. Followup of 44 patients in whom the tumor was resected showed that survival depended on tumor size. In four patients with tumors smaller than 1 cm without parenchymal invasion, the postoperative 5-yr cumulative survival rate was 100%. Pancreatic carcinoma smaller than 1 cm limited to duct epithelium is considered as early cancer. Various diagnostic imaging modalities are now available to evaluate patients in whom pancreatic carcinoma is clinically suspected. These include ultrasonography (US), computed tomography (CT), endoscopic retrograde cholangiopancreatography (ERCP), and angiography. More recently magnetic resonance imaging (MRI), endoscopic ultrasound (EUS), and peroral pancreatic ductal biopsy also have been used. This report compares diagnostic modalities for pancreatic carcinoma in order to provide a data base for their rational use in the diagnosis of small resectable pancreatic carcinomas.
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