1
|
Mukhopadhyay A, Bandyopadhyay S, Maulik U. Multi-class clustering of cancer subtypes through SVM based ensemble of pareto-optimal solutions for gene marker identification. PLoS One 2010; 5:e13803. [PMID: 21103052 PMCID: PMC2980474 DOI: 10.1371/journal.pone.0013803] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2009] [Accepted: 09/28/2010] [Indexed: 11/29/2022] Open
Abstract
With the advancement of microarray technology, it is now possible to study the expression profiles of thousands of genes across different experimental conditions or tissue samples simultaneously. Microarray cancer datasets, organized as samples versus genes fashion, are being used for classification of tissue samples into benign and malignant or their subtypes. They are also useful for identifying potential gene markers for each cancer subtype, which helps in successful diagnosis of particular cancer types. In this article, we have presented an unsupervised cancer classification technique based on multiobjective genetic clustering of the tissue samples. In this regard, a real-coded encoding of the cluster centers is used and cluster compactness and separation are simultaneously optimized. The resultant set of near-Pareto-optimal solutions contains a number of non-dominated solutions. A novel approach to combine the clustering information possessed by the non-dominated solutions through Support Vector Machine (SVM) classifier has been proposed. Final clustering is obtained by consensus among the clusterings yielded by different kernel functions. The performance of the proposed multiobjective clustering method has been compared with that of several other microarray clustering algorithms for three publicly available benchmark cancer datasets. Moreover, statistical significance tests have been conducted to establish the statistical superiority of the proposed clustering method. Furthermore, relevant gene markers have been identified using the clustering result produced by the proposed clustering method and demonstrated visually. Biological relationships among the gene markers are also studied based on gene ontology. The results obtained are found to be promising and can possibly have important impact in the area of unsupervised cancer classification as well as gene marker identification for multiple cancer subtypes.
Collapse
Affiliation(s)
- Anirban Mukhopadhyay
- Department of Computer Science and Engineering, University of Kalyani, Kalyani, West Bengal, India.
| | | | | |
Collapse
|
2
|
Jeong JK, Velho TAF, Mello CV. Cloning and expression analysis of retinoic acid receptors in the zebra finch brain. J Comp Neurol 2005; 489:23-41. [PMID: 15977168 DOI: 10.1002/cne.20605] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
The vitamin A derivative retinoic acid is produced postembryonically in discrete portions of the songbird brain, including some of the nuclei involved in song production and song learning, and its synthesis is required for the normal maturation of song behavior. To identify the brain targets for retinoic acid action, we cloned the zebra finch homologs of the alpha, beta, and gamma classes of retinoic acid receptors (RARs). In situ hybridization analysis revealed that the mRNAs for all three RARs are expressed at different levels in several brain areas, with a broader distribution than the mRNA for retinaldehyde-specific aldehyde dehydrogenase (zRalDH), a retinoic acid-synthesizing enzyme. Detectable RAR expression was found in all nuclei of the song control system, with the most marked expression occurring within the striatal song nucleus area X. These observations are consistent with a persistent action of retinoic acid in the postembryonic and adult songbird brain and provide further evidence for an involvement of retinoic acid signaling in the control of learned vocal behavior in a songbird species. They also suggest that the striatum is a major target of retinoic acid in songbirds.
Collapse
Affiliation(s)
- Jin K Jeong
- Neurological Sciences Institute, Oregon Health and Science University, West Campus, Beaverton, Oregon 97221, USA
| | | | | |
Collapse
|
3
|
Abel F, Sjöberg RM, Nilsson S, Kogner P, Martinsson T. Imbalance of the mitochondrial pro- and anti-apoptotic mediators in neuroblastoma tumours with unfavourable biology. Eur J Cancer 2005; 41:635-46. [PMID: 15737569 DOI: 10.1016/j.ejca.2004.12.021] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2004] [Revised: 11/17/2004] [Accepted: 12/17/2004] [Indexed: 11/24/2022]
Abstract
It has been proposed that a lack of apoptosis plays an important role in neuroblastoma (NB) progression. We therefore screened cDNA array filters, including 198 apoptotic genes, in order to identify mRNA transcripts that are differentially expressed in tumours with unfavourable versus favourable biology. Twenty-one genes were analysed further using real-time reverse-transcriptase-polymerase chain reaction (RT-PCR). Significantly lower levels of DNCL1 (PIN; P(c)(corrected) = 0.0054) and NTRK1 (TrkA; P(c) = 0.039) were found in NB tumours with unfavourable biology. In addition, BID, BCL2, APAF1, CASP2, CASP3 and CASP9 were found to be preferentially expressed in tumours with favourable biology, whereas CDKN1A (p21), IL2RA, and MCL1, were found to be preferentially expressed in NB tumours with unfavourable biology. In conclusion, mRNA levels of transcripts encoding pro-apoptotic mediators of the mitochondrial apoptotic pathway were found to be expressed to a lower extent in tumours with unfavourable biology. Our data also suggest that the mitochondrial pathway is suppressed in advanced stages of NB tumours, due to an imbalance between anti-apoptotic and pro-apoptotic mediators which is a finding that may have therapeutic significance.
Collapse
Affiliation(s)
- Frida Abel
- Department of Clinical Genetics, Gothenburg University, Sahlgrenska University Hospital/East, S-416 85 Gothenburg, Sweden
| | | | | | | | | |
Collapse
|
4
|
Qin P, Cimildoro R, Kochhar DM, Soprano KJ, Soprano DR. PBX, MEIS, and IGF-I are potential mediators of retinoic acid-induced proximodistal limb reduction defects. TERATOLOGY 2002; 66:224-34. [PMID: 12397630 DOI: 10.1002/tera.10082] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
BACKGROUND Phocomelia, which is primarily due to a disruption in the proximodistal axis, is found in virtually all mouse embryos exposed to high doses of retinoic acid (RA) on 11 days post coitum (dpc). METHODS To identify genes that potentially mediate the effects of retinoic acid (RA) on limb development, we have examined the expression of 9,000 clones from the IMAGE consortium by microarray analysis of RNA isolated from 11 dpc mouse forelimbs exposed to RA or vehicle for 6 hr. Eight genes that demonstrated altered expression were chosen for further study of their mRNA levels using RT-PCR. Protein levels were determined by Western blot analysis. RESULTS Of the 9,000 genes examined in the microarray, approximately 111 demonstrated altered expression (33 known genes and 78 ESTs). Of the eight known genes chosen for further study using RT-PCR, four mRNAs (PBX1a, PBX1b, IGF-Ia, and IGF-Ib) demonstrated consistent elevation ( approximately 3-fold) in their levels after RA treatment in both the forelimbs and hindlimbs as early as 3 hr after RA treatment. In addition to the two PBX1 isoforms, the mRNA level of the other two subtypes (PBX2 and PBX3) and the level of PBX1/2/3 protein were also found to be elevated in limb buds after RA treatment. Finally, we examined the expression of MEIS1, MEIS2, and MEIS3 because these proteins are necessary for PBX nuclear localization. The mRNA level of all three subtypes of MEIS were elevated approximately three- to four-fold in both the forelimbs and hindlimbs after RA treatment. CONCLUSIONS Because both PBX and MEIS (and their orthologs) are believed to be involved in the control of proximodistal axis formation in mouse and fly limbs and IGFs in the development of limbs, we suggest that increases in PBX, MEIS and IGF-1 mRNA levels may contribute to proximodistal limb reduction defects caused by teratogenic doses of RA.
Collapse
Affiliation(s)
- Pu Qin
- Department of Microbiology and Immunology, Temple University School of Medicine, Philadelphia, Pennsylvania 19122, USA
| | | | | | | | | |
Collapse
|
5
|
Abstract
In vitro studies that showed RA could cause growth arrest and differentiation of myelogenous leukemia and neuroblastoma led to clinical trials of retinoids in APL and neuroblastoma that increased survival for both of those diseases. In the case of APL, ATRA has been the drug of choice, and preclinical and clinical data support direct combinations of ATRA with cytotoxic chemotherapy. For neuroblastoma, a phase I study defined a dose of 13-cis-RA, which was tolerable in patients after myeloablative therapy, and a phase III trial that showed postconsolidation therapy with 13-cis-RA improved EFS for patients with high-risk neuroblastoma. Preclinical studies in neuroblastoma indicate that ATRA or 13-cis-RA can antagonize cytotoxic chemotherapy and radiation, so use of 13-cis-RA in neuroblastoma is limited to maintenance after completion of cytotoxic chemotherapy and radiation. A limitation on the antitumor benefit of ATRA in APL is the marked decrease in drug levels that occurs during therapy as a result of induction of drug metabolism, resulting in a shorter drug half-life and decreased plasma levels. Although early studies sought to overcome the pharmacologic limitations of ATRA therapy in APL, the demonstration that ATO is active against APL in RA-refractory patients has led to a focus on studies employing ATO. Use of 13-cis-RA in neuroblastoma has avoided the decreased plasma levels seen with ATRA. It is likely that recurrent disease seen during or after 13-cis-RA therapy in neuroblastoma is due to tumor cell resistance to retinoid-mediated differentiation induction. Studies in neuroblastoma cell lines resistant to 13-cis-RA and ATRA have shown that they can be sensitive, and in some cases collaterally hypersensitive, to the cytotoxic retinoid fenretinide. Fenretinide induces tumor cell cytotoxicity rather than differentiation, acts independently from RA receptors, and in initial phase I trials has been well tolerated. Clinical trials of fenretinide, alone and in combination with ceramide modulators, are in development.
Collapse
Affiliation(s)
- C P Reynolds
- Developmental Therapeutics Section, Division of Hematology-Oncology, Children's Hospital of Los Angeles, University of Southern California, Keck School of Medicine, Los Angeles, California, USA.
| | | |
Collapse
|
6
|
Abstract
The insulin-like growth factor (IGF) system includes IGF-I and IGF-II, the type I and type II IGF receptors, and specific IGF binding proteins (IGFBP-1 to IGFBP-6). These factors regulate both normal and malignant brain growth. Enhanced expression of IGF-I and IGF-II mRNA transcripts has been demonstrated in gliomas, meniningiomas, and other tumours. Abnormal imprinting of IGF-II occurs in gliomas, medulloblastomas, and meningiomas. Both types of IGF receptor are expressed in gliomas and, in particular, the type I IGF receptor appears to be upregulated in malignant brain tissue. Antisense IGF-I receptor mRNA induces an antitumour response, resulting in complete brain tumour regression. Clinical trials for the treatment of brain tumours in humans based on a gene transfer protocol using IGF-I receptor antisense are under way. All six IGFBPs are expressed to a variable extent in brain tumours. High concentrations of IGFBP-2 are found in cerebrospinal fluid from patients with malignant central nervous system tumours; therefore, IGFBP-2 might be a useful marker for these tumours. IGFBP-4 appears to be a negative regulator of tumour proliferation. Both in vitro and in vivo experiments suggest that the IGF system represents an important target for the treatment of malignant central nervous system tumours and the ongoing trials should provide valuable information for future therapeutic approaches.
Collapse
Affiliation(s)
- W Zumkeller
- Martin-Luther- University Halle-Wittenberg, University Hospital, Department of Pediatrics, Ernst-Grube-Str. 40, 06097 Halle/Saale, Germany.
| | | |
Collapse
|
7
|
Wasa M, Wang HS, Tazuke Y, Okada A. Insulin-like growth factor-I stimulates amino acid transport in a glutamine-deprived human neuroblastoma cell line. BIOCHIMICA ET BIOPHYSICA ACTA 2001; 1525:118-24. [PMID: 11342260 DOI: 10.1016/s0304-4165(00)00178-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
It is still unknown how insulin-like growth factor-I (IGF-I) regulates cancer cell growth in the condition of the limited availability of key nutrients, such as glutamine. We investigated the effects of IGF-I on cell growth and amino acid transport in a glutamine-deprived human neuroblastoma cell line, SK-N-SH. Cell growth was measured, and 3H-labeled amino acid transport was assayed after treatment with or without IGF-I (50 ng/ml) in 2 mM (control) and 100 microM glutamine concentrations. Cell growth rates were dependent on glutamine concentrations. IGF-I stimulated cell growth in both 2 mM and 100 microM glutamine. IGF-I stimulated glutamine transport in 100 microM glutamine with the mechanism of increasing carrier Vmax, but had no effect in 2 mM glutamine. IGF-I also stimulated leucine, glutamate and 2-(methylamino)isobutyric acid transport in 100 microM glutamine. There were significant increases in [3H]thymidine and [3H]leucine incorporation in IGF-I-treated cells in both 2 mM and 100 microM glutamine. These data suggest that IGF-I stimulates cell growth by increasing amino acid transport in the condition of low glutamine levels in a human neuroblastoma cell line. This mechanism may allow to maintain cell growth even in nutrient-deprived tumor tissues.
Collapse
Affiliation(s)
- M Wasa
- Department of Pediatric Surgery, Osaka University Graduate School of Medicine, 2-2 Yamadaoka, Suita, 565-0871, Osaka, Japan.
| | | | | | | |
Collapse
|
8
|
Denisenko-Nehrbass NI, Jarvis E, Scharff C, Nottebohm F, Mello CV. Site-specific retinoic acid production in the brain of adult songbirds. Neuron 2000; 27:359-70. [PMID: 10985355 DOI: 10.1016/s0896-6273(00)00043-x] [Citation(s) in RCA: 78] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
The song system of songbirds, a set of brain nuclei necessary for song learning and production, has distinctive morphological and functional properties. Utilizing differential display, we searched for molecular components involved in song system regulation. We identified a cDNA (zRalDH) that encodes a class 1 aldehyde dehydrogenase. zRalDH was highly expressed in various song nuclei and synthesized retinoic acid efficiently. Brain areas expressing zRalDH generated retinoic acid. Within song nucleus HVC, only projection neurons not undergoing adult neurogenesis expressed zRalDH. Blocking zRalDH activity in the HVC of juveniles interfered with normal song development. Our results provide conclusive evidence for localized retinoic acid synthesis in an adult vertebrate brain and indicate that the retinoic acid-generating system plays a significant role in the maturation of a learned behavior.
Collapse
Affiliation(s)
- N I Denisenko-Nehrbass
- Laboratory of Animal Behavior, The Rockefeller University, New York, New York 10021, USA
| | | | | | | | | |
Collapse
|
9
|
Bernardini S, Melino G, Cortese C, Ballerini S, Annicchiarico-Petruzzelli M, Bernassola F, Corazzari M, Federici G. Modulation of glutathione transferase P1-1 activity by retinoic acid in neuroblastoma cells. J Cell Biochem 1999. [DOI: 10.1002/(sici)1097-4644(19991201)75:3<375::aid-jcb3>3.0.co;2-i] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
|
10
|
Zeidman R, Löfgren B, Pâhlman S, Larsson C. PKCepsilon, via its regulatory domain and independently of its catalytic domain, induces neurite-like processes in neuroblastoma cells. J Cell Biol 1999; 145:713-26. [PMID: 10330401 PMCID: PMC2133186 DOI: 10.1083/jcb.145.4.713] [Citation(s) in RCA: 105] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
To investigate the role of protein kinase C (PKC) isoforms in regulation of neurite outgrowth, PKCalpha, betaII, delta, and epsilon fused to enhanced green fluorescent protein (EGFP) were transiently overexpressed in neuroblastoma cells. Overexpression of PKCepsilon-EGFP induced cell processes whereas the other isoforms did not. The effect of PKCepsilon-EGFP was not suppressed by the PKC inhibitor GF109203X. Instead, process formation was more pronounced when the regulatory domain was introduced. Overexpression of various fragments from PKCepsilon regulatory domain revealed that a region encompassing the pseudosubstrate, the two C1 domains, and parts of the V3 region were necessary and sufficient for induction of processes. By deleting the second C1 domain from this construct, a dominant-negative protein was generated which suppressed processes induced by full-length PKCepsilon and neurites induced during retinoic acid- and growth factor-induced differentiation. As with neurites in differentiated neuroblastoma cells, processes induced by the PKCepsilon- PSC1V3 protein contained alpha-tubulin, neurofilament-160, and F-actin, but the PKCepsilon-PSC1V3-induced processes lacked the synaptic markers synaptophysin and neuropeptide Y. These data suggest that PKCepsilon, through its regulatory domain, can induce immature neurite-like processes via a mechanism that appears to be of importance for neurite outgrowth during neuronal differentiation.
Collapse
Affiliation(s)
- R Zeidman
- Lund University, Department of Laboratory Medicine, Molecular Medicine, Malmö University Hospital, S-205 02 Malmö, Sweden
| | | | | | | |
Collapse
|
11
|
Melino G, De Laurenzi V, Catani MV, Terrinoni A, Ciani B, Candi E, Marekov L, Steinert PM. The cornified envelope: a model of cell death in the skin. Results Probl Cell Differ 1999; 24:175-212. [PMID: 9949837 DOI: 10.1007/978-3-540-69185-3_9] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- G Melino
- Department of Experimental Medicine, University of Rome Tor Vergata, Italy
| | | | | | | | | | | | | | | |
Collapse
|
12
|
Lovat PE, Irving H, Annicchiarico-Petruzzelli M, Bernassola F, Malcolm AJ, Pearson AD, Melino G, Redfern CP. Retinoids in neuroblastoma therapy: distinct biological properties of 9-cis- and all-trans-retinoic acid. Eur J Cancer 1997; 33:2075-80. [PMID: 9516856 DOI: 10.1016/s0959-8049(97)00242-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We investigated the potential for 9-cis-retinoic acid in the differentiation therapy of neuroblastoma using an N-type neuroblastoma cell line, SH SY 5Y, as an experimental model. In these cells, 9-cis-retinoic acid is more effective than other isomers at inducing the expression of RAR-beta. An RAR-alpha-specific antagonist inhibited the induction of RAR-beta in response to all-trans-but not to 9-cis-retinoic acid. This indicates that the mechanism of gene induction by 9-cis-retinoic acid differs markedly from all-trans-retinoic acid. 9-cis-retinoic acid is also better than all-trans at producing sustained morphological differentiation and inhibition of proliferation of SH SY 5Y cells. Although N-type neuroblastoma cells are not thought to undergo apoptosis in response to all-trans-retinoic acid, we observed a significant degree of apoptosis in SH SY 5Y cells treated with 9-cis-retinoic acid for 5 days and then cultured in the absence of retinoid, an effect not observed in cells treated with the all-trans isomer. These results suggest that 9-cis- and all-trans-retinoic acid have distinct biological properties and that 9-cis retinoic acid may be clinically effective in neuroblastoma by inducing both differentiation and apoptosis under an appropriate treatment regimen.
Collapse
Affiliation(s)
- P E Lovat
- Department of Medicine, University of Newcastle upon Tyne, U.K
| | | | | | | | | | | | | | | |
Collapse
|
13
|
Kiess W, Koepf G, Christiansen H, Blum WF. Human neuroblastoma cells use either insulin-like growth factor-I or insulin-like growth factor-II in an autocrine pathway via the IGF-I receptor: variability of IGF, IGF binding protein (IGFBP) and IGF receptor gene expression and IGF and IGFBP secretion in human neuroblastoma cells in relation to cellular proliferation. REGULATORY PEPTIDES 1997; 72:19-29. [PMID: 9404729 DOI: 10.1016/s0167-0115(97)01026-4] [Citation(s) in RCA: 25] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
Neuroblastoma cells are thought to depend upon autocrine stimulation by IGF-II but not by IGF-I. We have studied the expression of IGF, IGFBP and IGF receptor mRNA in two human neuroblastoma cell lines, SK-N-MC and CHP, and asked whether or not the expression of the IGF system in these malignant cells determines their growth pattern. SK-N-MC cells grow with a cell doubling time of 36 hours in medium supplemented with 10% fetal calf serum whereas CHP cells only grow with a doubling time of 72 h. In addition, the SK-N-MC cell line has a plating efficiency ten times greater than the CHP cell line. RNase protection assays were performed using (32)P-labelled riboprobes and RNA that had been purified from SK-N-MC and CHP cells respectively. A 520 bases human IGF-I, a 556 bases human IGF-II, a 480 bases human IGF-I receptor and a 250 human IGF-II/mannose-6-phosphate (M6P) receptor probe were radiolabelled as were human IGFBP-1, -2, -3, -4, -5 and -6 probes. While both SKNMC and CHP neuroblastoma cells expressed mRNAs for IGFBP-2, -4, and -6 no signal was detected for IGFBP-1, and -3 and only SK-N-MC cells expressed IGFBP-5 mRNA. In addition, a 400 bases protected band was seen with the IGF-I receptor probe and a 260 bases protected band with the IGF-IIM6P receptor probe in either cell line. Interestingly, a 300 bases protected species was detected with the IGF-II probe in CHP cell RNA whereas SK-N-MC cells did not express IGF-II transcripts. Conversely, SK-N-MC cells expressed a 520 bases IGF-I transcript while CHP cells did not show IGF-I mRNA expression. As determined by specific radioimmunoassays SK-N-MC cells secreted 0.75+/-0.02 ng/ml IGF-I, 1.2+/-0.04 ng/ml IGF-II and 149+/-2.1 ng/ml IGFBP-2 within 24 h, whereas CHP cells secreted 0.1+/-0.01 ng/ml IGF-I, but 6.2+/-0.1ng/ml IGF-II and 254.8+/-5.5 ng/ml IGFBP-2 (N=5). IGFBP-2 secretion correlated positively with IGF-II secretion in CHP cells (r=0.85, P=0.05) and negatively with IGF-I (r= -0.9, P<0.01) in SK-N-MC cells. In conclusion, SK-N-MC cells which grow rapidly and have a high plating efficiency, express IGF-I, while CHP cells that grow more slowly express IGF-II. We hypothesize that neuroblastoma cells depend upon autocrine stimulation by either IGF-I or IGF-II. Variable sensitivity to growth inhibitors or apoptotic processes may be related to the differential expression of the IGF system.
Collapse
MESH Headings
- Autocrine Communication
- Blotting, Western
- Cell Division
- Culture Media, Conditioned
- DNA, Complementary/genetics
- DNA, Complementary/metabolism
- Electrophoresis, Polyacrylamide Gel
- Gene Expression Regulation, Neoplastic
- Humans
- Insulin-Like Growth Factor Binding Proteins/genetics
- Insulin-Like Growth Factor Binding Proteins/metabolism
- Insulin-Like Growth Factor I/genetics
- Insulin-Like Growth Factor I/metabolism
- Insulin-Like Growth Factor II/genetics
- Insulin-Like Growth Factor II/metabolism
- Neuroblastoma/genetics
- Neuroblastoma/metabolism
- Neuroblastoma/pathology
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- Radioimmunoassay
- Receptor, IGF Type 1/genetics
- Receptor, IGF Type 1/immunology
- Ribonucleases/metabolism
- Tumor Cells, Cultured
Collapse
Affiliation(s)
- W Kiess
- Children's Hospital, Justus Liebig University of Giessen, Germany.
| | | | | | | |
Collapse
|
14
|
Kaba SE, Kyritsis AP, Conrad C, Gleason MJ, Newman R, Levin VA, Yung WK. The treatment of recurrent cerebral gliomas with all-trans-retinoic acid (tretinoin). J Neurooncol 1997; 34:145-51. [PMID: 9210061 DOI: 10.1023/a:1005743707803] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Malignant gliomas continue to be a significant source of mortality in young and middle aged adults. The introduction of new treatment strategies and multidisciplinary approaches has improved the outcome of patients with these tumors only slightly. Because retinoic acid has growth inhibitory activity against glioma and neuroblastoma cells in cultures, we assessed the efficacy of all-trans-retinoic acid in the treatment of recurrent cerebral gliomas. Thirty-six patients with recurrent cerebral gliomas were entered in the study and treated with 120 or 150 mg/ m2/day of all-trans-retinoic acid as a single agent. The drug was given for 3 weeks followed with one week of rest. Two blocks of 4 weeks constituted one course of treatment. One (3%) of 34 evaluable patients had a minor response and 14 (41%) had stable disease. In the rest of the patients (56%), tumors continued to progress despite treatment. The median time to progression of all evaluable patients was 8 weeks, and for the responders was 17 weeks. The higher dose level (150 mg/m2) was associated with high incidence of headache, which responded to dose reduction. The lower dose level was very well tolerated, with mild, mainly dermatological toxicity. All-trans-retinoic acid as a single agent has no significant activity against recurrent cerebral gliomas.
Collapse
Affiliation(s)
- S E Kaba
- Department of Neuro-oncology, University of Texas M.D. Anderson Cancer Center, Houston, USA
| | | | | | | | | | | | | |
Collapse
|
15
|
Melino G, Draoui M, Bellincampi L, Bernassola F, Bernardini S, Piacentini M, Reichert U, Cohen P. Retinoic acid receptors alpha and gamma mediate the induction of "tissue" transglutaminase activity and apoptosis in human neuroblastoma cells. Exp Cell Res 1997; 235:55-61. [PMID: 9281352 DOI: 10.1006/excr.1997.3656] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
All-trans retinoic acid (RA) reduces human neuroblastoma growth by inducing either differentiation or apoptosis. The apoptotic program in these cells is regulated by RA and is paralleled by the transcriptional induction of "tissue" transglutaminase (tTG). tTG is a protein cross-linking enzyme, which specifically accumulates in cells undergoing apoptosis in various in vivo and in vitro systems. In neuroblastoma cells, tTG is detected exclusively in the cells expressing the S-type phenotype and showing an increased apoptosis. The present study was undertaken to identify the retinoid receptors which are involved in the regulation of tTG and apoptosis as well as in the in vitro neuronal differentiation of the human SK-N-BE(2) neuroblastoma cell line. We have previously characterized the retinoid acid receptors expressed in this cell line. In the present study, by using synthetic retinoids selectively activating RAR/RXR isoforms, we have identified the RAR/RXR receptors involved in the induction of either apoptosis or differentiation. We have also studied the effect of the selective RA analogs on tTG activity. We observed that while RARalpha- and RARgamma-selective retinoids alone were able to induce tTG activity, only the combined stimulation of both RARalpha and RARgamma induced apoptosis. Conversely, several combinations of RAR/RXR closely mimicked the differentiation effects observed with all-trans retinoic acid. These results indicate that, at variance with differentiation, the induction of apoptosis in human SK-N-BE(2) neuroblastoma cells is under the specific control of RARalpha and RARgamma. These data seem relevant for the reported ability of RARgamma to suppress the clinically malignant tumor phenotype in patients.
Collapse
Affiliation(s)
- G Melino
- c/o Department of Experimental Medicine, Istituto Dermopatico dell'Immacolata (IDI-IRCCS), Rome, Tor Vergata, Italy
| | | | | | | | | | | | | | | |
Collapse
|
16
|
Bernardini S, Melino G, Saura F, Annicchiarico-Petruzzelli M, Motti C, Cortese C, Federici G. Expression of co-factors (SMRT and Trip-1) for retinoic acid receptors in human neuroectodermal cell lines. Biochem Biophys Res Commun 1997; 234:278-82. [PMID: 9169003 DOI: 10.1006/bbrc.1997.6626] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
Retinoic acid (RA) induces growth inhibition, differentiation or cell death in many human neuroblastoma cell lines. Recently, the transactivation activity of nuclear retinoids receptors has been shown to be modulated through physical association with other proteins that act as co-activators or as co-repressors. We investigated the expression of the co-repressor (SMRT) and co-activator (Trip 1) for retinoid and thyroid-hormone receptors in several neuroectodermal tumour cell lines, and its modulation by all-trans-retinoic acid, as well as by synthetic agonists, for RAR alpha, RAR beta, RAR gamma and RXR. We demonstrate that (i) SMRT and Trip-1 mRNAs are expressed in many human neuroblastoma and melanoma cell lines in basal conditions, (ii) SMRT mRNA expression in human neuroblastoma cell line SK-N-BE(2) increases after 48 hours of incubation with 1 microM RA and RARs specific agonists, (iii) Trip-1 mRNA in the same cell line does not change during incubation with RA or selective synthetic agonists for RARs and RXR.
Collapse
Affiliation(s)
- S Bernardini
- Post Graduate School in Biochemistry and Clinical Chemistry, University of Camerino, Rome, Italy
| | | | | | | | | | | | | |
Collapse
|
17
|
Lovat PE, Irving H, Annicchiarico-Petruzzelli M, Bernassola F, Malcolm AJ, Pearson AD, Melino G, Redfern CP. Apoptosis of N-type neuroblastoma cells after differentiation with 9-cis-retinoic acid and subsequent washout. J Natl Cancer Inst 1997; 89:446-52. [PMID: 9091647 DOI: 10.1093/jnci/89.6.446] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
BACKGROUND The overall survival rate for patients with neuroblastoma has improved over the past two decades, but long-term survival for the subgroup of patients with high-risk disease remains low. In recent years, there has been interest in the potential clinical use of drugs able to induce differentiation of neuroblastoma cells. Since 9-cis-retinoic acid induces better and more sustained differentiation of neuroblastoma in vitro than other retinoic acid isomers, this may be a more appropriate retinoid for use in neuroblastoma therapy. PURPOSE The purpose of this work was to compare the long-term effects of all-trans- and 9-cis-retinoic acid on neuroblastoma differentiation using an N-type (neuroblastic) cell line, SH SY 5Y, as an in vitro model. In addition, we wanted to find out whether 9-cis-retinoic acid would induce programmed cell death (apoptosis) in these N-type neuroblastoma cells and to determine whether the effects of either 9-cis- or all-trans-retinoic acid are dependent on their continued presence in the culture medium. METHODS SH SY 5Y cells were incubated in either the continued presence of all-trans- or 9-cis-retinoic acid or for 5 days with retinoic acid followed by culture in the absence of retinoid for up to 13 days. Morphologic changes were observed using phase-contrast and scanning electron microscopy. Apoptosis was determined by flow cytometry of propidium iodide-stained cells and by using terminal deoxynucleotidyl transferase to end-label DNA fragments in situ in apoptotic cells. RESULTS Culture of SH SY 5Y cells with all-trans- or 9-cis retinoic acid for 5 days induced morphologic differentiation and inhibited cell growth. These effects were maintained in the continuous presence of each retinoic acid isomer but were more profound in cells treated with 9-cis-retinoic acid. The differentiation of cells treated with all-trans-retinoic acid was reversible once retinoic acid was removed from the medium. Conversely, apoptosis was induced in cells treated with 9-cis-retinoic acid for 5 days and cultured for 9 days (4 days after washout) but not in cells cultured in the continuous presence of 9-cis-retinoic acid. This effect was specific to 9-cis-retinoic acid. CONCLUSIONS Previous studies have demonstrated differential responses to all-trans-retinoic acid in N- and S-type (substrate-adherent or Schwann-like) neuroblastoma cells: Apoptosis is induced in S-type cells, whereas differentiation occurs in N-type cells. The present results show that, unlike all-trans-retinoic acid, 9-cis-retinoic acid induces both differentiation and apoptosis in N-type SH SY 5Y neuroblastoma cells. However, apoptosis was dependent on removal of 9-cis-retinoic acid from the culture medium. IMPLICATIONS Since both differentiation and apoptosis are involved in tumor regression, 9-cis-retinoic acid may be a more appropriate retinoid for clinical trials in neuroblastoma. The dependence of apoptosis on treatment and subsequent removal of 9-cis-retinoic acid implies that drug scheduling may be an important parameter affecting therapeutic efficacy.
Collapse
Affiliation(s)
- P E Lovat
- Department of Medicine, University of Newcastle Upon Tyne, U.K
| | | | | | | | | | | | | | | |
Collapse
|
18
|
Melino G, Thiele CJ, Knight RA, Piacentini M. Retinoids and the control of growth/death decisions in human neuroblastoma cell lines. J Neurooncol 1997; 31:65-83. [PMID: 9049832 DOI: 10.1023/a:1005733430435] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Cell proliferation, the balance between mitosis and apoptosis is the result of the continuous integration of a number of different signal transduction pathways stimulated in a cell at any given point in its life. Neuroblastoma cells regulate the switch between mitosis and death, according both to intrinsic factors and extrinsic factors, such as growth factor withdrawal and action of the vitamin A derivative, retinoic acid. In this review, we describe the balance of some factors regulating growth and death of human neuroblastoma cells in vitro. These dynamic studies are necessarily-performed on cell lines, which offer controlled conditions enabling the disection of the complex stimuli mediating survival and growth (IGF, trk, BDNF) and death (transglutaminase, free radicals, Bcl-2). Although the conclusions drawn may therefore not be directly applicable to tumour cells in vivo, the results herein discussed are of sufficient significance to warrant in vivo relevance.
Collapse
Affiliation(s)
- G Melino
- IDI-IRCCS Biochemistry Lab., Dept. Experimental Medicine, University of Rome Tor Vergata, Italy
| | | | | | | |
Collapse
|
19
|
Lupulescu A. The role of hormones, growth factors and vitamins in carcinogenesis. Crit Rev Oncol Hematol 1996; 23:95-130. [PMID: 8835851 DOI: 10.1016/1040-8428(96)00198-9] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- A Lupulescu
- Wayne State University, School of Medicine, Detroit, MI, USA
| |
Collapse
|
20
|
Ratka A, Flores BM, Mambourg SE, Torian BE. Luteinizing hormone-releasing hormone in undifferentiated and differentiated SK-N-SH human neuroblastoma cells. Neuropeptides 1996; 30:87-94. [PMID: 8868305 DOI: 10.1016/s0143-4179(96)90060-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
The presence of luteinizing hormone-releasing hormone (LHRH) in SK-N-SH human neuroblastoma cells was investigated by immunocytochemistry and enzyme-linked immunosorbent assays of whole cell extracts and culture medium. In addition, ribonuclease protection assays were utilized to quantitate LHRH messenger RNA. The expression of LHRH mRNA and LHRH protein level was correlated with neuronal differentiation induced by retinoic acid (RA). In differentiated SK-N-SH cells the LHRH mRNA level as well as the amount of LHRH in cell extracts and cell medium were significantly lower than in differentiated cells. These results suggest that RA affects the expression of LHRH mRNA and the level of LHRH protein in SK-N-SH cells. These data show that altering the growth state of the human neuroblastoma SK-N-SH cells toward more neuronal phenotype results in a significant decrease in expression of LHRH mRNA and the protein. The ability of RA to induce changes in LHRH at the mRNA and at the peptide levels will allow further study of RA regulation of LHRH at the neuronal level.
Collapse
Affiliation(s)
- A Ratka
- Department of Pharmaceutical Sciences, Idaho State University, Pocatello 83209, USA
| | | | | | | |
Collapse
|
21
|
Bernardini S, Cianfarani S, Spagnoli A, Annicchiarico-Petruzzelli M, Melino G, Massoud R, Boscherini B, Finazzi-Agró A, Rosenfeld RG, Federici G. Expression and down-regulation by retinoic acid of IGF binding protein-2 and -4 in medium from human neuroblastoma cells. J Neuroendocrinol 1994; 6:409-13. [PMID: 7527270 DOI: 10.1111/j.1365-2826.1994.tb00601.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
Insulin-like growth factors (IGFs) regulate the autocrine/paracrine growth of neuroblastomas. The IGFs bind to specific binding proteins (IGFBPs) which modulate their biological activity. We investigated, by Western ligand blotting (WLB), the presence of IGFBPs and their possible modulation by retinoic acid (RA), IGF-I, IGF-II and truncated Des(1-3)IGF-I in conditioned medium (CM) of the human neuroblastoma SK-N-BE(2) cell line. We demonstrated the presence of two IGFBPs, with MW 37 kDa and 25 kDa. Following immunoprecipitation, they turned out to be IGFBP-2 and -4, respectively. The RA-induced differentiation in SK-N-BE(2) cells was accompanied by a marked reduction of the intensity of both IGFBP bands after 48 h (32% and 24% of control, respectively) and 72 h (2% and 0% of control, respectively) incubation. The addition of exogenous IGFs, which did not induce cell differentiation, did not change the IGFBP pattern significantly, except for the truncated form of IGF-I, which induced a marked decrease in both the 37 kDa and 25 kDa bands after 72 h incubation (45% and 18% of control, respectively). These findings suggest that IGFBPs have a role in RA-induced differentiation in human neuroblastoma cells.
Collapse
Affiliation(s)
- S Bernardini
- Department of Biology, University of Rome Tor Vergata, Italy
| | | | | | | | | | | | | | | | | | | |
Collapse
|
22
|
Lovat PE, Pearson AD, Malcolm A, Redfern CP. Retinoic acid receptor expression during the in vitro differentiation of human neuroblastoma. Neurosci Lett 1993; 162:109-13. [PMID: 8121610 DOI: 10.1016/0304-3940(93)90572-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Neuroblastoma cells differentiate in response to retinoic acid and cyclic AMP. We have examined the expression of retinoic acid receptors (RARs) in relation to neuroblastoma differentiation and show that short term exposure of SK N SH, SH SY 5Y AND GI LI N cells to physiological concentrations of retinoic acid results in induction of RAR-beta, particularly the lower transcript. Cyclic AMP has no effect on retinoic acid mediated induction and does not alter RAR expression patterns. These data are discussed in the light of evidence that retinoic acid and cyclic AMP act either on different control pathways or at different points within a common pathway.
Collapse
Affiliation(s)
- P E Lovat
- Department of Child Health, University of Newcastle, UK
| | | | | | | |
Collapse
|