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Ma’ayeh SY, Brook-Carter PT. Representational difference analysis identifies specific genes in the interaction of Giardia duodenalis with the murine intestinal epithelial cell line, IEC-6. Int J Parasitol 2012; 42:501-9. [DOI: 10.1016/j.ijpara.2012.04.004] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2012] [Revised: 03/30/2012] [Accepted: 04/02/2012] [Indexed: 10/28/2022]
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Patzke S, Hauge H, Sioud M, Finne EF, Sivertsen EA, Delabie J, Stokke T, Aasheim HC. Identification of a novel centrosome/microtubule-associated coiled-coil protein involved in cell-cycle progression and spindle organization. Oncogene 2005; 24:1159-73. [PMID: 15580290 DOI: 10.1038/sj.onc.1208267] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Here we describe the identification of a novel vertebrate-specific centrosome/spindle pole-associated protein (CSPP) involved in cell-cycle regulation. The protein is predicted to have a tripartite domain structure, where the N- and C-terminal domains are linked through a coiled-coil mid-domain. Experimental analysis of the identified domains revealed that spindle association is dependent on the N-terminal and the coiled-coil mid domain. The expression of CSPP at the mRNA level was detected in all tested cell lines and in testis tissue. Ectopic expression of CSPP in HEK293T cells blocked cell-cycle progression in early G1 phase and in mitosis in a dose-dependent manner. Interestingly, mitosis-arrested cells contained aberrant spindles and showed impairment of chromosome congression. Inhibition of CSPP gene expression by small interfering RNAs induced cell-cycle arrest/delay in S phase. This phenotype was characterized by elevated levels of cyclin A, decreased levels of cyclin E and hyperphosphorylation of the S-phase checkpoint kinase Chk1. The activation of Chk1 may indicate a replication stress response due to an inappropriate G1/S-phase transition. Taken together, we demonstrate that CSPP is associated with centrosomes and microtubules and may play a role in the regulation of G(1)/S-phase progression and spindle assembly.
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Affiliation(s)
- Sebastian Patzke
- Department of Immunology, The Norwegian Radium Hospital, Montebello, 0310 Oslo, Norway
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Hauge H, Patzke S, Delabie J, Aasheim HC. Characterization of a novel immunoglobulin-like domain containing receptor. Biochem Biophys Res Commun 2004; 323:970-8. [PMID: 15381095 DOI: 10.1016/j.bbrc.2004.08.188] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2004] [Indexed: 10/26/2022]
Abstract
A not yet described gene was identified in a lymphoma specific subtraction strategy. Three splice variants of this gene denoted immunoglobulin-like domain containing receptor 1 (ILDR1) were identified and characterized. Cellular localization studies showed membrane-association for two of the variants, while the third was cytoplasmic and appeared to translocate to the membrane upon co-expression with any of the other two isoforms. ILDR1 shows approximately 30% homology to a recently described protein from rat, lipolysis stimulated receptor, that has been shown to bind low-density lipoprotein. The gene encoding ILDR1 is localized to chromosome 3q21.1 and it is expressed in prostate, testis, pancreas, kidney, liver, and heart. Interestingly, the shortest transcript corresponding to the cytoplasmic variant could only be detected in lymphoma samples and not in normal tissues or cell lines tested. The expression of this variant may therefore be related to the development and/or progression of cancer.
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Affiliation(s)
- Helena Hauge
- Department of Immunology, The Norwegian Radium Hospital, Oslo, Norway
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Skretting G, Espenes A, Ulvund MJ, Olsaker I. cDNA representational difference analysis of ileal Peyer’s patches in lambs after oral inoculation with scrapie. Biochem Biophys Res Commun 2004; 316:272-9. [PMID: 15003541 DOI: 10.1016/j.bbrc.2004.02.040] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2003] [Indexed: 11/28/2022]
Abstract
cDNA representational difference analysis (RDA) was used to study gene expression profiles in the ileal Peyer's patch of a lamb 1 week after oral inoculation with the scrapie agent. Twenty-five differentially expressed cDNA fragments were identified and cloned. Sequence analysis indicated seven novel gene sequences. Other clones shared sequence homology with genes encoding ribosomal and mitochondrial proteins, the translation initiation factor EIF4GII and the bovine pancreatic thread protein. Reverse Northern was used to confirm the differential expression in another four lambs inoculated with scrapie and the tissue distribution of the novel genes was examined using Northern blot analysis.
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Affiliation(s)
- Grethe Skretting
- Department of Basic Sciences and Aquatic Medicine, Norwegian School of Veterinary Science, P.O. Box 8146 Dep., N-0033 Oslo, Norway.
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Boräng S, Andersson T, Thelin A, Odeberg J, Lundeberg J. Vascular Gene Expression in Atherosclerotic Plaque-Prone Regions Analyzed by Representational Difference Analysis. Pathobiology 2004; 71:107-14. [PMID: 14707446 DOI: 10.1159/000074426] [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: 11/22/2002] [Accepted: 06/06/2003] [Indexed: 11/19/2022] Open
Abstract
OBJECTIVES Atherosclerotic plaques are known to develop and progress where the endothelium is subjected to turbulent blood flow. We have applied cDNA representational difference analysis (RDA) to study vascular gene expression in mouse aorta in a model for atherosclerosis. METHODS Gene expression profiles were investigated in plaque-prone and plaque-resistant localizations in the ascending aorta and arch in 8-week-old ApoE-/- and LDLR-/- mice. Total RNA was extracted and two rounds of subtraction were performed; the difference products were characterized in detail by shotgun cloning and analysis of more than 2,700 gene sequences. RESULTS The identified differentially expressed gene sequences include both genes with known involvement in vascular gene expression and genes previously not implicated in vascular processes. For example, CD36 and caveolin, previously reported for their participation in the progression of atherosclerosis, were found to have an increased expression in vessel localizations thought to be especially susceptible to plaque formation. CONCLUSIONS This report provides new in vivo information of expressed genes that can be useful for further investigations of the molecular mechanisms in focal localization of atherosclerosis.
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Affiliation(s)
- Stina Boräng
- Department of Biotechnology, KTH, Royal Institute of Technology, Stockholm, Sweden
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Bønsdorff T, Eggen A, Gautier M, Asheim HC, Rønningen K, Lingaas F, Olsaker I. Identification and physical mapping of genes expressed in the corpus luteum in cattle. Anim Genet 2004; 34:325-33. [PMID: 14510667 DOI: 10.1046/j.1365-2052.2003.01023.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
A representational difference analysis was performed to identify genes expressed in the corpus luteum of cattle. The corpus luteum is an ovarian structure that is essential for the establishment and maintenance of pregnancy. Knowledge of gene expression and function of corpus luteum will be important to improve fertility in humans and domestic animals. Housekeeping genes were removed from the corpus luteum representation (tester) using skeletal muscle as the subtracting agent (driver). A total of 80 clones of the final subtraction product were analysed by sequencing and 11 new bovine gene sequences were identified (pBTCL1-11). The sequences were mapped to segments of 10 different chromosomes using a somatic cell hybrid panel and a radiation hybrid panel. With one exception the locations are in agreement with published comparative maps of cattle and man. Expression in corpus luteum was verified by RT-PCR for all the 11 clones.
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Affiliation(s)
- T Bønsdorff
- Department of Morphology, Genetics and Aquatic Biology, Norwegian School of Veterinary Science, Oslo, Norway
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Linder K, Arner P, Flores-Morales A, Tollet-Egnell P, Norstedt G. Differentially expressed genes in visceral or subcutaneous adipose tissue of obese men and women. J Lipid Res 2003; 45:148-54. [PMID: 14563828 DOI: 10.1194/jlr.m300256-jlr200] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
There is growing evidence that the distribution of adipose tissue in the body is of importance in the development of metabolic complications of obesity, such as diabetes, hypertension, and hyperlipidemia. The aim of this study was to identify differentially expressed genes in subcutaneous and omental human adipose tissue in obese men, using a subtractive hybridization strategy. From the obtained set of differentially expressed transcripts, we also aimed to identify genes that have a sex-specific pattern of expression in omental or subcutaneous adipose tissue. Representational difference analysis (RDA) was performed on cDNA from subcutaneous and omental fat tissue from a man with extreme abdominal obesity. Forty-four putatively differentially expressed genes were identified. The obtained RDA products were spotted onto glass slides to screen for differential expression in other obese patients by using a microarray hybridization procedure. Five genes were confirmed to be differentially expressed in subcutaneous or omental adipose tissue from male or female obese patients. One gene was detected only in males and was found to be upregulated in subcutaneous tissue. The findings extend previous knowledge that different fat depots have differential gene expression and indicate that sex differences exist in adipose gene expression patterns.
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Affiliation(s)
- Kristina Linder
- Department of Molecular Medicine, Karolinska Hospital, Stockholm, Sweden.
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Andersson T, Boräng S, Unneberg P, Wirta V, Thelin A, Lundeberg J, Odeberg J. Shotgun sequencing and microarray analysis of RDA transcripts. Gene 2003; 310:39-47. [PMID: 12801631 DOI: 10.1016/s0378-1119(03)00498-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Monitoring of differential gene expression is an important step towards understanding of gene function. We describe a comparison of the representational difference analysis (RDA) subtraction process with corresponding microarray analysis. The subtraction steps are followed in a quantitative manner using a shotgun cloning and sequencing procedure that includes over 1900 gene sequences. In parallel, the enriched transcripts are spotted onto microarrays facilitating large scale hybridization analysis of the representations and the difference products. We show by the shotgun procedure that there is a high diversity of gene fragments represented in the iterative RDA products (92-67% singletons) with a low number of shared sequences (<9%) between subsequent subtraction cycles. A non redundant set of 1141 RDA clones were immobilized on glass slides and the majority of these clones (97%) gave repeated good fluorescent signals in a subsequent hybridization of the labelled and amplified original cDNA. We observed only a low number of false positives (<2%) and a more than twofold differential expression for 32% (363) of the immobilized RDA clones. In conclusion, we show that by random sequencing of the difference products we obtained an accurate transcript profile of the individual steps and that large-scale confirmation of the obtained transcripts can be achieved by microarray analysis.
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Affiliation(s)
- Tove Andersson
- Department of Biotechnology, Division of Molecular Biotechnology, KTH, Royal Institute of Technology, AlbaNova University Center, Stockholm Centre for Physics, Astronomy, and Biotechnology, SE-106 91, Stockholm, Sweden
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Patzke S, Lindeskog M, Munthe E, Aasheim HC. Characterization of a novel human endogenous retrovirus, HERV-H/F, expressed in human leukemia cell lines. Virology 2002; 303:164-73. [PMID: 12482668 DOI: 10.1006/viro.2002.1615] [Citation(s) in RCA: 40] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
We have identified and characterized a human endogenous retrovirus (HERV) gag transcript in the human pre-B cell leukemia line Reh. The transcript was found to be a splice product of a structurally intact HERV element located on chromosome 6q13. Its primer binding site is complementary to phenylalanine (F) tRNA, common for the HERV-F family, but the overall genome sequence is closely related to the HERV-H family. The retroviral sequence was therefore designated HERV-H/F. The HERV element shows a distinct mRNA expression pattern among hematopoietic cancer cell lines with expression in some leukemia-derived cell lines of B-lymphoid and myeloid origin. No expression was observed in normal human tissues, indicating a cancer-specific expression pattern. The 5' long terminal repeat (LTR) was tested for promoter activity in HERV-H/F expressing and nonexpressing cell lines. The cell specificity of the LTR-mediated reporter gene expression did not conclusively correlate with endogenous virus expression, indicating that the transcription regulation of this gene is not alone dependent on cell-specific activity of transcription factors.
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Affiliation(s)
- Sebastian Patzke
- The Norwegian Radium Hospital, Department of Immunology, Montebello, N-0310, Oslo, Norway
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Dillner K, Kindblom J, Flores-Morales A, Pang ST, Törnell J, Wennbo H, Norstedt G. Molecular characterization of prostate hyperplasia in prolactin-transgenic mice by using cDNA representational difference analysis. Prostate 2002; 52:139-49. [PMID: 12111705 DOI: 10.1002/pros.10102] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
BACKGROUND Transgenic mice overexpressing the rat prolactin (PRL) gene develop a dramatic enlargement of the prostate gland. The objective of this study was to characterize the molecular mechanisms in the prostate of importance for the prostate hyperplasia seen in these transgenic mice. METHODS cDNA representational difference analysis (cDNA RDA) was used to isolate differentially expressed transcripts in the prostate hyperplasia of the transgenic mice compared with wildtype littermates. Furthermore, cDNA microarray analysis was used to verify the RDA output. RESULTS Here we report 10 transcripts, some of them described to be involved in proliferation and apoptosis, which are differentially expressed in the enlarged transgenic prostates compared with controls. CONCLUSION The identified differentially expressed transcripts presented herein supports molecular similarities between the prostate hyperplasia of PRL-transgenic mice and human BPH that may contribute to explain the molecular basis of prostate hyperplasia.
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Affiliation(s)
- Karin Dillner
- Department of Pharmacology and Physiology, Göteborg University, Göteborg, Sweden.
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Boräng S, Andersson T, Thelin A, Larsson M, Odeberg J, Lundeberg J. Monitoring of the subtraction process in solid-phase representational difference analysis: characterization of a candidate drug. Gene 2001; 271:183-92. [PMID: 11418239 DOI: 10.1016/s0378-1119(01)00486-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
In this study, we have applied and evaluated a modified cDNA representational difference analysis (RDA) protocol based on magnetic bead technology to study the molecular effects of a candidate drug (N,N'-diacetyl-L-cystine, DiNAC) in a model for atherosclerosis. Alterations in a gene expression profile induced by DiNAC were investigated in a human monocytic cell line (THP-1) differentiated into macrophage-like cells by lipopolysaccharide and further exposed to DiNAC. Three rounds of subtraction have been performed and the difference products from the second and third rounds have been characterized in detail by analysis of over 1000 gene sequences. Two protocols for analysis of the subtraction products have been evaluated, a shotgun approach and size selection of both distinct fragments and band-patterned smear. We demonstrate that in order to obtain a representative view of the most abundant gene fragments, the shotgun procedure is preferred. The obtained sequences were analyzed against the UniGene and Expressed Gene Anatomy Database (EGAD) databases and the results were visualized and analyzed with the ExProView software enabling rapid pair-wise comparison and identification of individual genes or functional groups of genes with altered expression levels. The identified differentially expressed gene sequences were comprised of both genes with known involvement in atherosclerosis or cholesterol biosynthesis and genes previously not implicated in these processes. The applicability of a solid-phase shotgun RDA protocol, combined with virtual chip monitoring, results in new starting points for characterization of novel candidate drugs.
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Affiliation(s)
- S Boräng
- Department of Biotechnology, KTH Royal Institute of Technology, Teknikringen 34, S-100 44 Stockholm, Sweden
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