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Loginov VI, Dmitriev AA, Senchenko VN, Pronina IV, Khodyrev DS, Kudryavtseva AV, Krasnov GS, Gerashchenko GV, Chashchina LI, Kazubskaya TP, Kondratieva TT, Lerman MI, Angeloni D, Braga EA, Kashuba VI. Tumor Suppressor Function of the SEMA3B Gene in Human Lung and Renal Cancers. PLoS One 2015; 10:e0123369. [PMID: 25961819 PMCID: PMC4427300 DOI: 10.1371/journal.pone.0123369] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2014] [Accepted: 02/05/2015] [Indexed: 12/26/2022] Open
Abstract
The SEMA3B gene is located in the 3p21.3 LUCA region, which is frequently affected in different types of cancer. The objective of our study was to expand our knowledge of the SEMA3B gene as a tumor suppressor and the mechanisms of its inactivation. In this study, several experimental approaches were used: tumor growth analyses and apoptosis assays in vitro and in SCID mice, expression and methylation assays and other. With the use of the small cell lung cancer cell line U2020 we confirmed the function of SEMA3B as a tumor suppressor, and showed that the suppression can be realized through the induction of apoptosis and, possibly, associated with the inhibition of angiogenesis. In addition, for the first time, high methylation frequencies have been observed in both intronic (32-39%) and promoter (44-52%) CpG-islands in 38 non-small cell lung carcinomas, including 16 squamous cell carcinomas (SCC) and 22 adenocarcinomas (ADC), and in 83 clear cell renal cell carcinomas (ccRCC). Correlations between the methylation frequencies of the promoter and the intronic CpG-islands of SEMA3B with tumor stage and grade have been revealed for SCC, ADC and ccRCC. The association between the decrease of the SEMA3B mRNA level and hypermethylation of the promoter and the intronic CpG-islands has been estimated in renal primary tumors (P < 0.01). Using qPCR, we observed on the average 10- and 14-fold decrease of the SEMA3B mRNA level in SCC and ADC, respectively, and a 4-fold decrease in ccRCC. The frequency of this effect was high in both lung (92-95%) and renal (84%) tumor samples. Moreover, we showed a clear difference (P < 0.05) of the SEMA3B relative mRNA levels in ADC with and without lymph node metastases. We conclude that aberrant expression and methylation of SEMA3B could be suggested as markers of lung and renal cancer progression.
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MESH Headings
- Animals
- Carcinoma, Renal Cell/genetics
- Carcinoma, Renal Cell/pathology
- Cell Line, Tumor
- CpG Islands
- DNA Methylation
- Gene Expression Regulation, Neoplastic
- Humans
- Kidney/metabolism
- Kidney/pathology
- Kidney Neoplasms/genetics
- Kidney Neoplasms/pathology
- Lung/metabolism
- Lung/pathology
- Lung Neoplasms/genetics
- Lung Neoplasms/pathology
- Membrane Glycoproteins/genetics
- Mice, SCID
- Neoplasms, Squamous Cell/genetics
- Neoplasms, Squamous Cell/pathology
- Neovascularization, Pathologic/genetics
- Neovascularization, Pathologic/pathology
- Promoter Regions, Genetic
- Semaphorins/genetics
- Small Cell Lung Carcinoma/genetics
- Small Cell Lung Carcinoma/pathology
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Affiliation(s)
- Vitaly I. Loginov
- Laboratory of Pathogenomics and Transcriptomics, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315, Moscow, Russia
- Laboratory of Molecular Genetics of Complex Inherited Diseases, Research Center of Medical Genetics, Russian Academy of Medical Sciences, 115478, Moscow, Russia
| | - Alexey A. Dmitriev
- Laboratory of Structural and Functional Genomics, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
- Department of Pathomorphology, P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, 125284, Moscow, Russia
| | - Vera N. Senchenko
- Laboratory of Structural and Functional Genomics, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
| | - Irina V. Pronina
- Laboratory of Pathogenomics and Transcriptomics, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315, Moscow, Russia
- Laboratory of Molecular Genetics of Complex Inherited Diseases, Research Center of Medical Genetics, Russian Academy of Medical Sciences, 115478, Moscow, Russia
| | - Dmitry S. Khodyrev
- Laboratory of Genetics, Federal Research Clinical Center of Federal Medical and Biological Agency of Russia, 115682, Moscow, Russia
| | - Anna V. Kudryavtseva
- Laboratory of Structural and Functional Genomics, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
- Department of Pathomorphology, P.A. Herzen Moscow Cancer Research Institute, Ministry of Healthcare of the Russian Federation, 125284, Moscow, Russia
| | - George S. Krasnov
- Laboratory of Structural and Functional Genomics, Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, 119991, Moscow, Russia
- Laboratory of Biotechnology, Mechnikov Research Institute for Vaccines and Sera, Russian Academy of Medical Sciences, 105064, Moscow, Russia
| | - Ganna V. Gerashchenko
- Department of Molecular Oncogenetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680, Kiev, Ukraine
| | - Larisa I. Chashchina
- Department of Molecular Oncogenetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680, Kiev, Ukraine
| | - Tatiana P. Kazubskaya
- Research Institute of Clinical Oncology, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, 115478, Moscow, Russia
| | - Tatiana T. Kondratieva
- Research Institute of Clinical Oncology, N.N. Blokhin Cancer Research Center, Russian Academy of Medical Sciences, 115478, Moscow, Russia
| | | | - Debora Angeloni
- The Institute of Life Sciences, Scuola Superiore Sant'Anna, 56127, Pisa, Italy
- Institute of Clinical Physiology, National Research Council, 56124, Pisa, Italy
- Istituto Toscano Tumori, 56124, Pisa, Italy
| | - Eleonora A. Braga
- Laboratory of Pathogenomics and Transcriptomics, Institute of General Pathology and Pathophysiology, Russian Academy of Medical Sciences, 125315, Moscow, Russia
- Laboratory of Molecular Genetics of Complex Inherited Diseases, Research Center of Medical Genetics, Russian Academy of Medical Sciences, 115478, Moscow, Russia
- Laboratory of Post Genomic Molecular Genetic Research, Institute of Biochemical Physics, Russian Academy of Sciences, 119334, Moscow, Russia
| | - Vladimir I. Kashuba
- Department of Molecular Oncogenetics, Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 03680, Kiev, Ukraine
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, SE-17177, Stockholm, Sweden
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Characterization of Two Human Lung Adenocarcinoma Cell Lines by Reciprocal Chromosome Painting. Zool Res 2010; 31:113-21. [DOI: 10.3724/sp.j.1141.2010.02113] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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Wang F, Grigorieva EV, Li J, Senchenko VN, Pavlova TV, Anedchenko EA, Kudryavtseva AV, Tsimanis A, Angeloni D, Lerman MI, Kashuba VI, Klein G, Zabarovsky ER. HYAL1 and HYAL2 inhibit tumour growth in vivo but not in vitro. PLoS One 2008; 3:e3031. [PMID: 18725949 PMCID: PMC2516603 DOI: 10.1371/journal.pone.0003031] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2008] [Accepted: 08/02/2008] [Indexed: 12/11/2022] Open
Abstract
Background We identified two 3p21.3 regions (LUCA and AP20) as most frequently affected in lung, breast and other carcinomas and reported their fine physical and gene maps. It is becoming increasingly clear that each of these two regions contains several TSGs. Until now TSGs which were isolated from AP20 and LUCA regions (e.g.G21/NPRL2, RASSF1A, RASSF1C, SEMA3B, SEMA3F, RBSP3) were shown to inhibit tumour cell growth both in vitro and in vivo. Methodology/Principal Findings The effect of expression HYAL1 and HYAL2 was studied by colony formation inhibition, growth curve and cell proliferation tests in vitro and tumour growth assay in vivo. Very modest growth inhibition was detected in vitro in U2020 lung and KRC/Y renal carcinoma cell lines. In the in vivo experiment stably transfected KRC/Y cells expressing HYAL1 or HYAL2 were inoculated into SCID mice (10 and 12 mice respectively). Tumours grew in eight mice inoculated with HYAL1. Ectopic HYAL1 was deleted in all of them. HYAL2 was inoculated into 12 mice and only four tumours were obtained. In 3 of them the gene was deleted. In one tumour it was present but not expressed. As expected for tumour suppressor genes HYAL1 and HYAL2 were down-expressed in 15 fresh lung squamous cell carcinomas (100%) and clear cell RCC tumours (60–67%). Conclusions/Significance The results suggest that the expression of either gene has led to inhibition of tumour growth in vivo without noticeable effect on growth in vitro. HYAL1 and HYAL2 thus differ in this aspect from other tumour suppressors like P53 or RASSF1A that inhibit growth both in vitro and in vivo. Targeting the microenvironment of cancer cells is one of the most promising venues of cancer therapeutics. As major hyaluronidases in human cells, HYAL1 and HYAL2 may control intercellular interactions and microenvironment of tumour cells providing excellent targets for cancer treatment.
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Affiliation(s)
- Fuli Wang
- Microbiology and Tumour Biology Center, Karolinska Institute, Stockholm, Sweden
| | - Elvira V. Grigorieva
- Microbiology and Tumour Biology Center, Karolinska Institute, Stockholm, Sweden
- Institute of Molecular Biology and Biophysics, SD RAMS, Novosibirsk, Russia
| | - Jingfeng Li
- Microbiology and Tumour Biology Center, Karolinska Institute, Stockholm, Sweden
| | - Vera N. Senchenko
- Engelhardt Institute of Molecular Biology, Russian Acad. Sciences, Moscow, Russia
| | - Tatiana V. Pavlova
- Microbiology and Tumour Biology Center, Karolinska Institute, Stockholm, Sweden
- Engelhardt Institute of Molecular Biology, Russian Acad. Sciences, Moscow, Russia
| | | | - Anna V. Kudryavtseva
- Engelhardt Institute of Molecular Biology, Russian Acad. Sciences, Moscow, Russia
| | | | - Debora Angeloni
- Cancer-Causing Genes Section, Laboratory of Immunobiology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
- Scuola Superiore Sant'Anna and Institute of Clinical Physiology – CNR, Pisa, Italy
| | - Michael I. Lerman
- Cancer-Causing Genes Section, Laboratory of Immunobiology, Center for Cancer Research, National Cancer Institute, Frederick, Maryland, United States of America
| | - Vladimir I. Kashuba
- Microbiology and Tumour Biology Center, Karolinska Institute, Stockholm, Sweden
- Institute of Molecular Biology and Genetics, Ukrainian Academy of Sciences, Kiev, Ukraine
| | - George Klein
- Microbiology and Tumour Biology Center, Karolinska Institute, Stockholm, Sweden
| | - Eugene R. Zabarovsky
- Microbiology and Tumour Biology Center, Karolinska Institute, Stockholm, Sweden
- * E-mail:
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Darai-Ramqvist E, Sandlund A, Müller S, Klein G, Imreh S, Kost-Alimova M. Segmental duplications and evolutionary plasticity at tumor chromosome break-prone regions. Genome Res 2008; 18:370-9. [PMID: 18230801 DOI: 10.1101/gr.7010208] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
We have previously found that the borders of evolutionarily conserved chromosomal regions often coincide with tumor-associated deletion breakpoints within human 3p12-p22. Moreover, a detailed analysis of a frequently deleted region at 3p21.3 (CER1) showed associations between tumor breaks and gene duplications. We now report on the analysis of 54 chromosome 3 breaks by multipoint FISH (mpFISH) in 10 carcinoma-derived cell lines. The centromeric region was broken in five lines. In lines with highly complex karyotypes, breaks were clustered near known fragile sites, FRA3B, FRA3C, and FRA3D (three lines), and in two other regions: 3p12.3-p13 ( approximately 75 Mb position) and 3q21.3-q22.1 ( approximately 130 Mb position) (six lines). All locations are shown based on NCBI Build 36.1 human genome sequence. The last two regions participated in three of four chromosome 3 inversions during primate evolution. Regions at 75, 127, and 131 Mb positions carry a large ( approximately 250 kb) segmental duplication (tumor break-prone segmental duplication [TBSD]). TBSD homologous sequences were found at 15 sites on different chromosomes. They were located within bands frequently involved in carcinoma-associated breaks. Thirteen of them have been involved in inversions during primate evolution; 10 were reused by breaks during mammalian evolution; 14 showed copy number polymorphism in man. TBSD sites showed an increase in satellite repeats, retrotransposed sequences, and other segmental duplications. We propose that the instability of these sites stems from specific organization of the chromosomal region, associated with location at a boundary between different CG-content isochores and with the presence of TBSDs and "instability elements," including satellite repeats and retroviral sequences.
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Affiliation(s)
- Eva Darai-Ramqvist
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institute, Stockholm SE-171 77, Sweden
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Darai-Ramqvist E, de Ståhl TD, Sandlund A, Mantripragada K, Klein G, Dumanski J, Imreh S, Kost-Alimova M. Array-CGH and multipoint FISH to decode complex chromosomal rearrangements. BMC Genomics 2006; 7:330. [PMID: 17196103 PMCID: PMC1769374 DOI: 10.1186/1471-2164-7-330] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2006] [Accepted: 12/29/2006] [Indexed: 11/13/2022] Open
Abstract
Background Recently, several high-resolution methods of chromosome analysis have been developed. It is important to compare these methods and to select reliable combinations of techniques to analyze complex chromosomal rearrangements in tumours. In this study we have compared array-CGH (comparative genomic hybridization) and multipoint FISH (mpFISH) for their ability to characterize complex rearrangements on human chromosome 3 (chr3) in tumour cell lines. We have used 179 BAC/PAC clones covering chr3 with an approximately 1 Mb resolution to analyze nine carcinoma lines. Chr3 was chosen for analysis, because of its frequent rearrangements in human solid tumours. Results The ploidy of the tumour cell lines ranged from near-diploid to near-pentaploid. Chr3 locus copy number was assessed by interphase and metaphase mpFISH. Totally 53 chr3 fragments were identified having copy numbers from 0 to 14. MpFISH results from the BAC/PAC clones and array-CGH gave mainly corresponding results. Each copy number change on the array profile could be related to a specific chromosome aberration detected by metaphase mpFISH. The analysis of the correlation between real copy number from mpFISH and the average normalized inter-locus fluorescence ratio (ANILFR) value detected by array-CGH demonstrated that copy number is a linear function of parameters that include the variable, ANILFR, and two constants, ploidy and background normalized fluorescence ratio. Conclusion In most cases, the changes in copy number seen on array-CGH profiles reflected cumulative chromosome rearrangements. Most of them stemmed from unbalanced translocations. Although our chr3 BAC/PAC array could identify single copy number changes even in pentaploid cells, mpFISH provided a more accurate analysis in the dissection of complex karyotypes at high ploidy levels.
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Affiliation(s)
- Eva Darai-Ramqvist
- Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, S-17177, Stockholm, Sweden
| | - Teresita Diaz de Ståhl
- Department of Pathology, Rudbeck Laboratory, Uppsala University Hospital, S-75185, Uppsala, Sweden
| | - Agneta Sandlund
- Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, S-17177, Stockholm, Sweden
| | - Kiran Mantripragada
- Department of Pathology, Rudbeck Laboratory, Uppsala University Hospital, S-75185, Uppsala, Sweden
| | - George Klein
- Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, S-17177, Stockholm, Sweden
| | - Jan Dumanski
- Howell and Elizabeth Heflin Center for Human Genetics, University of Alabama at Birmingham (UAB), Medical School, Birmingham, AL 35294-0024, USA
| | - Stefan Imreh
- Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, S-17177, Stockholm, Sweden
| | - Maria Kost-Alimova
- Department of Microbiology, Tumour and Cell Biology (MTC), Karolinska Institutet, S-17177, Stockholm, Sweden
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Li J, Wang F, Haraldson K, Protopopov A, Duh FM, Geil L, Kuzmin I, Minna JD, Stanbridge E, Braga E, Kashuba VI, Klein G, Lerman MI, Zabarovsky ER. Functional characterization of the candidate tumor suppressor gene NPRL2/G21 located in 3p21.3C. Cancer Res 2004; 64:6438-43. [PMID: 15374952 DOI: 10.1158/0008-5472.can-03-3869] [Citation(s) in RCA: 62] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Initial analysis identified the NPRL2/G21 gene located in 3p21.3C, the lung cancer region, as a strong candidate tumor suppressor gene. Here we provide additional evidence of the tumor suppressor function of NPRL2/G21. The gene has highly conserved homologs/orthologs ranging from yeast to humans. The yeast ortholog, NPR2, shows three highly conserved regions with 32 to 36% identity over the whole length. By sequence analysis, the main product of NPRL2/G21 encodes a soluble protein that has a bipartite nuclear localization signal, a protein-binding domain, similarity to the MutS core domain, and a newly identified nitrogen permease regulator 2 domain with unknown function. The gene is highly expressed in many tissues. We report inactivating mutations in a variety of tumors and cancer cell lines, growth suppression of tumor cells with tet-controlled NPRL2/G21 transgenes on plastic Petri dishes, and suppression of tumor formation in SCID mice. Screening of 7 renal, 5 lung, and 7 cervical carcinoma cell lines showed homozygous deletions in the 3' end of NPRL2 in 2 renal, 3 lung, and 1 cervical (HeLa) cell line. Deletions in the 3' part of NPRL2 could result in improper splicing, leading to the loss of the 1.8 kb functional NPRL2 mRNA. We speculate that the NPRL2/G21 nuclear protein may be involved in mismatch repair, cell cycle checkpoint signaling, and activation of apoptotic pathway(s). The yeast NPR2 was shown to be a target of cisplatin, suggesting that the human NPRL2/G21 may play a similar role. At least two homozygous deletions of NPRL2/G21 were detected in 6 tumor biopsies from various locations and with microsatellite instability. This study, together with previously obtained results, indicates that NPRL2 is a multiple tumor suppressor gene.
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Affiliation(s)
- Jingfeng Li
- Microbiology and Tumor Biology Center, Center for Genomics and Bioinformatics, Karolinska Institute, Stockholm, Sweden
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Mao L. Molecular abnormalities in lung carcinogenesis and their potential clinical implications. Lung Cancer 2001; 34 Suppl 2:S27-34. [PMID: 11720738 DOI: 10.1016/s0169-5002(01)00341-5] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Development of lung cancer is multistep and requires accumulation of multiple genetic and epigenetic alterations. Modern molecular technology has facilitated a rapid and effective identification of these genetic alterations as well as epigenetic alterations. The determination of molecular alterations in the early tumorigenic process of the lung will not only extend our understanding of the underlying biology but also provide molecular markers for cancer risk assessment, early detection, and molecular classification. In this article, I will discuss the common molecular abnormalities in lung cancer and how these abnormalities may be used as biomarkers in clinical practice.
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Affiliation(s)
- L Mao
- The University of Texas M.D. Anderson Cancer Center, FC9.3014, 1515 Holcombe Blvd, Houston, TX 77030, USA.
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Ogilvie CM, Shemilt S, Davies AF, Weber-Hall S, Chuang C, Sundaresan V. Characterization of a chromosomally complex lung cancer cell line using multiwell fluorescence in situ hybridization. CANCER GENETICS AND CYTOGENETICS 2000; 117:149-52. [PMID: 10704688 DOI: 10.1016/s0165-4608(99)00148-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The chromosomal characterization of a non-small cell lung cancer cell line (NCIH358) is described. This characterization was achieved using a simple, cheap and technically straightforward multiwell fluorescence in situ hybridization (FISH) method. The many and complex chromosome rearrangements identified by this method could not be defined using conventional G-banded chromosome analysis, and have not been previously described. For the detailed characterization of complex cell lines, multiwell FISH has many advantages over more technically demanding and expensive FISH techniques, and opens up the possibility of screening for consistent rearrangements, leading to the identification of unique fusion genes.
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Affiliation(s)
- C M Ogilvie
- Department of Cytogenetics, Guy's & St. Thomas' Hospital Trust, London, United Kingdom
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