34 results on '"Caramuta, S"'
Search Results
2. Cost-effectiveness analysis of VEGF-A testing to predict response to bevacizumab (BEV) as a component of neo-adjuvant therapy of early HER-2 negative breast cancer
- Author
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Blank, P.R., primary, Loibl, S., additional, Linderholm, B.K., additional, Caramuta, S., additional, Nekljudova, V., additional, Szucs, T.D., additional, Van Stiphout, J., additional, Ademi, Z., additional, von Minckwitz, G., additional, and Schwenkglenks, M., additional
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- 2015
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3. microRNA expression signatures of gastrointestinal stromal tumours: associations with imatinib resistance and patient outcome
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Akçakaya, P, primary, Caramuta, S, additional, Åhlen, J, additional, Ghaderi, M, additional, Berglund, E, additional, Östman, A, additional, Bränström, R, additional, Larsson, C, additional, and Lui, W-O, additional
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- 2014
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4. Gene expression profiling of advanced ovarian cancer: characterizazion of a molecular signature involving the fibroblast growth factor 2 signaling
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Bertuletti, M., Bussani, E., Canevari, A., Caramuta, S., Daidone, M., DE CECCO, L., Delia, D., Ditto, A., Ferrario, C., Gariboldi, M., Lagonigro, S., Marchionni, L., Mezzanzanica, D., Oggionni, M., Pierotti, M., Pilotti, S, Raspagliesi, A., Reid, J., Schneider, Claudio, and Turatti, F.
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- 2004
5. Role of microRNAs and microRNA machinery in the pathogenesis of diffuse large B-cell lymphoma
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Caramuta, S, primary, Lee, L, additional, Özata, D M, additional, Akçakaya, P, additional, Georgii-Hemming, P, additional, Xie, H, additional, Amini, R-M, additional, Lawrie, C H, additional, Enblad, G, additional, Larsson, C, additional, Berglund, M, additional, and Lui, W-O, additional
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- 2013
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6. 732 Role of microRNAs and microRNA machinery in the pathogenesis of diffuse large B-cell lymphomas
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Caramuta, S., primary, Berglund, M., additional, Özata, D., additional, Akçakaya, P., additional, Georgii-Hemming, P., additional, Xie, H., additional, Enblad, G., additional, Larsson, C., additional, and Lui, W.O., additional
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- 2010
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7. 889 The involvement of miR-483 and its host gene IGF2 in development of adrenal cortical carcinoma
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Ozata, D., primary, Caramuta, S., additional, Akcakaya, P., additional, Xie, H.O.N.G., additional, Bäckdahl, M., additional, Larsson, C., additional, and Lui, W., additional
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- 2010
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8. 739 Altered expression of miR-205 affects cell proliferation in human cervical cancer
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Xie, H., primary, Caramuta, S., additional, Larsson, C., additional, and Lui, W.O., additional
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- 2010
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9. Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays
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Pourmand, N., primary, Caramuta, S., additional, Villablanca, A., additional, Mori, S., additional, Karhanek, M., additional, Wang, S. X., additional, and Davis, R. W., additional
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- 2007
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10. Branch migration displacement assay with automated heuristic analysis for discrete DNA length measurement using DNA microarrays
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Shan X. Wang, Stefano Caramuta, Ronald W. Davis, Silvia Mori, Miloslav Karhanek, Andrea Villablanca, Nader Pourmand, Pourmand, N, Caramuta, S, Villablanca, A, Mori, S, Karhanek, M, Wang, S, and Davis, R
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Forensic Genetics ,STR multiplex system ,DNA fingerprinting ,Oligonucleotides ,Computational biology ,Biology ,Forensic Genetic ,Nucleic acid thermodynamics ,Sequencing by hybridization ,Genetic ,Oligonucleotide ,Multiplex ,Short tandem repeat ,Oligonucleotide Array Sequence Analysis ,Genetics ,Multidisciplinary ,Oligonucleotide Array Sequence Analysi ,Nucleic Acid Hybridization ,DNA ,Biological Sciences ,DNA profiling ,Neural Networks (Computer) ,Branch migration ,STR analysis ,Microsatellite Repeat ,Neural Networks, Computer ,DNA microarray ,Microsatellite Repeats - Abstract
The analysis of short tandem repeats (STRs) plays an important role in forensic science, human identification, genetic mapping, and disease diagnostics. Traditional STR analysis utilizes gel- or column-based approaches to analyze DNA repeats. Individual STR alleles are separated and distinguished according to fragment length; thus the assay is generally hampered by its low multiplex capacity. However, use of DNA microarray would employ a simple hybridization and detection for field forensics and biology. Here we demonstrate a rapid, highly sensitive method for STR analysis that utilizes DNA microarray technology. We describe two adaptations to accomplish this: the use of competitive hybridization to remove unpaired ssDNA from an array and the use of neural network classification to automate the analysis. The competitive displacement technique mimics the branch migration process that occurs during DNA recombination. Our technique will facilitate the rapid deduction of identity, length, and number of repeats for the multiple STRs in an unknown DNA sample. © 2007 by The National Academy of Sciences of the USA
- Published
- 2007
11. Altered expression of the IGF2‑H19 locus and mitochondrial respiratory complexes in adrenocortical carcinoma.
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Scicluna P, Caramuta S, Kjellin H, Xu C, Fröbom R, Akhtar M, Gao J, Shi H, Kjellman M, Almgren M, Höög A, Zedenius J, Ekström TJ, Bränström R, Lui WO, and Larsson C
- Subjects
- Electron Transport Complex I metabolism, Humans, Insulin-Like Growth Factor II genetics, Insulin-Like Growth Factor II metabolism, NAD metabolism, Ubiquinone, Adrenal Cortex Neoplasms genetics, Adrenal Cortex Neoplasms pathology, Adrenocortical Adenoma metabolism, Adrenocortical Adenoma pathology, Adrenocortical Carcinoma genetics, Adrenocortical Carcinoma pathology, MicroRNAs genetics
- Abstract
Abnormalities of the insulin‑like growth factor 2 (IGF2)‑H19 locus with the overexpression of IGF2 are frequent findings in adrenocortical carcinoma (ACC). The present study assessed the expression of RNAs and microRNAs (miRNAs/miRs) from the IGF2‑H19 locus using PCR‑based methods in ACC and adrenocortical adenoma (ACA). The results were associated with proteomics data. IGF2 was overexpressed in ACC, and its expression correlated with that of miR‑483‑3p and miR‑483‑5p hosted by IGF2 . The downregulated expression of H19 in ACC compared to ACA correlated with miR‑675 expression hosted by H19 . Several proteins exhibited an inverse correlation in expression and were predicted as targets of miR‑483‑3p , miR‑483‑5p or miR‑675 . Subsets of these proteins were differentially expressed between ACC and ACA. These included several proteins involved in mitochondrial metabolism. Among the mitochondrial respiratory complexes, complex I and IV were significantly decreased in ACC compared to ACA. The protein expression of NADH:ubiquinone oxidoreductase subunit C1 (NDUFC1), a subunit of mitochondrial respiratory complex I, was further validated as being lower in ACC compared to ACA and normal adrenals. The silencing of miR‑483‑5p increased NDUFC1 protein expression and reduced both oxygen consumption and glycolysis rates. On the whole, the findings of the present study reveal the dysregulation of the IGF2‑H19 locus and mitochondrial respiration in ACC. These findings may provide a basis for the further understanding of the pathogenesis of ACC and may have potential values for diagnostics and treatment.
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- 2022
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12. Imatinib Regulates miR-483-3p and Mitochondrial Respiratory Complexes in Gastrointestinal Stromal Tumors.
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Huang WK, Shi H, Akçakaya P, Zeljic K, Gangaev A, Caramuta S, Yeh CN, Bränström R, Larsson C, and Lui WO
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- Antineoplastic Agents therapeutic use, Cell Line, Tumor, Cell Survival drug effects, Cell Survival genetics, Down-Regulation drug effects, Gastrointestinal Neoplasms drug therapy, Gastrointestinal Neoplasms genetics, Gastrointestinal Neoplasms pathology, Gastrointestinal Stromal Tumors drug therapy, Gastrointestinal Stromal Tumors genetics, Gastrointestinal Stromal Tumors pathology, Gene Expression Regulation, Neoplastic drug effects, Humans, Imatinib Mesylate therapeutic use, MicroRNAs genetics, Mitochondria drug effects, Oxidative Phosphorylation drug effects, RNA, Messenger genetics, Signal Transduction genetics, Transfection, Antineoplastic Agents pharmacology, Electron Transport Complex II metabolism, Gastrointestinal Neoplasms metabolism, Gastrointestinal Stromal Tumors metabolism, Imatinib Mesylate pharmacology, MicroRNAs metabolism, Mitochondria enzymology, Signal Transduction drug effects
- Abstract
Metabolic adaptation to increased oxidative phosphorylation (OXPHOS) has been found in gastrointestinal stromal tumor (GIST) upon imatinib treatment. However, the underlying mechanism of imatinib-induced OXPHOS is unknown. Discovering molecules that mediate imatinib-induced OXPHOS may lead to the development of therapeutic strategies synergizing the efficacy of imatinib. In this study, we explored the role of microRNAs in regulating OXPHOS in GIST upon imatinib treatment. Using a microarray approach, we found that miR-483-3p was one of the most downregulated miRNAs in imatinib-treated tumors compared to untreated tumors. Using an extended series of GIST samples, we further validated the downregulation of miR-483-3p in imatinib-treated GIST samples by RT-qPCR. Using both gain- and loss-of-function experiments, we showed that miR-483-3p could regulate mitochondrial respiratory Complex II expression, suggesting its role in OXPHOS regulation. Functionally, miR-483-3p overexpression could rescue imatinib-induced cell death. These findings provide the molecular link for imatinib-induced OXPHOS expression and the biological role of miR-483-3p in regulating cell viability upon imatinib treatment.
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- 2021
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13. Proteomics identifies neddylation as a potential therapy target in small intestinal neuroendocrine tumors.
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Fotouhi O, Kjellin H, Juhlin CC, Pan Y, Vesterlund M, Ghaderi M, Yousef A, Andersson-Sand H, Kharaziha P, Caramuta S, Kjellman M, Zedenius J, Larsson C, and Orre LM
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- Aged, Apoptosis drug effects, Carrier Proteins metabolism, Cell Line, Tumor, Cyclopentanes pharmacology, Cyclopentanes therapeutic use, Female, Humans, Male, Middle Aged, NEDD8 Protein metabolism, Proliferating Cell Nuclear Antigen metabolism, Proteomics methods, Pyrimidines pharmacology, Pyrimidines therapeutic use, RNA, Small Interfering metabolism, Ubiquitins metabolism, Intestinal Neoplasms drug therapy, Intestinal Neoplasms metabolism, Intestine, Small drug effects, Intestine, Small metabolism, Neuroendocrine Tumors drug therapy, Neuroendocrine Tumors metabolism
- Abstract
Patients with small intestinal neuroendocrine tumors (SI-NETs) frequently develop spread disease; however, the underlying molecular mechanisms of disease progression are not known and effective preventive treatment strategies are lacking. Here, protein expression profiling was performed by HiRIEF-LC-MS in 14 primary SI-NETs from patients with and without liver metastases detected at the time of surgery and initial treatment. Among differentially expressed proteins, overexpression of the ubiquitin-like protein NEDD8 was identified in samples from patients with liver metastasis. Further, NEDD8 correlation analysis indicated co-expression with RBX1, a key component in cullin-RING ubiquitin ligases (CRLs). In vitro inhibition of neddylation with the therapeutic agent pevonedistat (MLN4924) resulted in a dramatic decrease of proliferation in SI-NET cell lines. Subsequent mass spectrometry-based proteomics analysis of pevonedistat effects and effects of the proteasome inhibitor bortezomib revealed stabilization of multiple targets of CRLs including p27, an established tumor suppressor in SI-NET. Silencing of NEDD8 and RBX1 using siRNA resulted in a stabilization of p27, suggesting that the cellular levels of NEDD8 and RBX1 affect CRL activity. Inhibition of CRL activity, by either NEDD8/RBX1 silencing or pevonedistat treatment of cells resulted in induction of apoptosis that could be partially rescued by siRNA-based silencing of p27. Differential expression of both p27 and NEDD8 was confirmed in a second cohort of SI-NET using immunohistochemistry. Collectively, these findings suggest a role for CRLs and the ubiquitin proteasome system in suppression of p27 in SI-NET, and inhibition of neddylation as a putative therapeutic strategy in SI-NET.
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- 2019
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14. Targeting CDK2 overcomes melanoma resistance against BRAF and Hsp90 inhibitors.
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Azimi A, Caramuta S, Seashore-Ludlow B, Boström J, Robinson JL, Edfors F, Tuominen R, Kemper K, Krijgsman O, Peeper DS, Nielsen J, Hansson J, Egyhazi Brage S, Altun M, Uhlen M, and Maddalo G
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- Bridged Bicyclo Compounds, Heterocyclic pharmacology, Cell Line, Tumor, Cell Survival drug effects, Cyclic N-Oxides, Cyclin-Dependent Kinase 2 genetics, Gene Expression Regulation, Neoplastic drug effects, HSP90 Heat-Shock Proteins antagonists & inhibitors, Humans, Indolizines, Melanoma drug therapy, Melanoma genetics, Microphthalmia-Associated Transcription Factor genetics, Phosphoproteins metabolism, Proteomics, Pyridinium Compounds pharmacology, Up-Regulation, Azabicyclo Compounds pharmacology, Cyclin-Dependent Kinase 2 metabolism, Drug Resistance, Neoplasm drug effects, Imidazoles pharmacology, Melanoma metabolism, Microphthalmia-Associated Transcription Factor metabolism, Oximes pharmacology, Phthalic Acids pharmacology
- Abstract
Novel therapies are undergoing clinical trials, for example, the Hsp90 inhibitor, XL888, in combination with BRAF inhibitors for the treatment of therapy-resistant melanomas. Unfortunately, our data show that this combination elicits a heterogeneous response in a panel of melanoma cell lines including PDX-derived models. We sought to understand the mechanisms underlying the differential responses and suggest a patient stratification strategy. Thermal proteome profiling (TPP) identified the protein targets of XL888 in a pair of sensitive and unresponsive cell lines. Unbiased proteomics and phosphoproteomics analyses identified CDK2 as a driver of resistance to both BRAF and Hsp90 inhibitors and its expression is regulated by the transcription factor MITF upon XL888 treatment. The CDK2 inhibitor, dinaciclib, attenuated resistance to both classes of inhibitors and combinations thereof. Notably, we found that MITF expression correlates with CDK2 upregulation in patients; thus, dinaciclib would warrant consideration for treatment of patients unresponsive to BRAF-MEK and/or Hsp90 inhibitors and/or harboring MITF amplification/overexpression., (© 2018 The Authors. Published under the terms of the CC BY 4.0 license.)
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- 2018
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15. Silencing FLI or targeting CD13/ANPEP lead to dephosphorylation of EPHA2, a mediator of BRAF inhibitor resistance, and induce growth arrest or apoptosis in melanoma cells.
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Azimi A, Tuominen R, Costa Svedman F, Caramuta S, Pernemalm M, Frostvik Stolt M, Kanter L, Kharaziha P, Lehtiö J, Hertzman Johansson C, Höiom V, Hansson J, and Egyhazi Brage S
- Subjects
- Antineoplastic Agents therapeutic use, Apoptosis drug effects, Apoptosis genetics, CD13 Antigens antagonists & inhibitors, CD13 Antigens metabolism, Cell Cycle Checkpoints drug effects, Cell Cycle Checkpoints genetics, Cell Line, Tumor, Dasatinib therapeutic use, Drug Resistance, Neoplasm drug effects, Drug Resistance, Neoplasm genetics, Ephrin-A2 metabolism, Humans, Indoles therapeutic use, Melanoma drug therapy, Melanoma metabolism, Melanoma pathology, Microfilament Proteins genetics, Microfilament Proteins metabolism, Phosphorylation, Protein Kinase Inhibitors therapeutic use, Proto-Oncogene Proteins B-raf antagonists & inhibitors, Proto-Oncogene Proteins B-raf metabolism, Proto-Oncogene Proteins c-akt genetics, Proto-Oncogene Proteins c-akt metabolism, Proto-Oncogene Proteins c-met genetics, Proto-Oncogene Proteins c-met metabolism, Pyridones therapeutic use, Pyrimidinones therapeutic use, RNA, Small Interfering genetics, RNA, Small Interfering metabolism, Receptor, EphA2, Receptors, Cytoplasmic and Nuclear genetics, Receptors, Cytoplasmic and Nuclear metabolism, Ribosomal Protein S6 Kinases, 90-kDa genetics, Ribosomal Protein S6 Kinases, 90-kDa metabolism, Signal Transduction, Skin Neoplasms drug therapy, Skin Neoplasms metabolism, Skin Neoplasms pathology, Sulfonamides therapeutic use, Trans-Activators, Vemurafenib, CD13 Antigens genetics, Ephrin-A2 genetics, Gene Expression Regulation, Neoplastic, Melanoma genetics, Microfilament Proteins antagonists & inhibitors, Proto-Oncogene Proteins B-raf genetics, Receptors, Cytoplasmic and Nuclear antagonists & inhibitors, Skin Neoplasms genetics
- Abstract
A majority of patients with BRAF-mutated metastatic melanoma respond to therapy with BRAF inhibitors (BRAFi), but relapses are common owing to acquired resistance. To unravel BRAFi resistance mechanisms we have performed gene expression and mass spectrometry based proteome profiling of the sensitive parental A375 BRAF V600E-mutated human melanoma cell line and of daughter cell lines with induced BRAFi resistance. Increased expression of two novel resistance candidates, aminopeptidase-N (CD13/ANPEP) and ETS transcription factor FLI1 was observed in the BRAFi-resistant daughter cell lines. In addition, increased levels of the previously reported resistance mediators, receptor tyrosine kinase ephrine receptor A2 (EPHA2) and the hepatocyte growth factor receptor MET were also identified. The expression of these proteins was assessed in matched tumor samples from melanoma patients obtained before BRAFi and after disease progression. MET was overexpressed in all progression samples while the expression of the other candidates varied between the individual patients. Targeting CD13/ANPEP by a blocking antibody induced apoptosis in both parental A375- and BRAFi-resistant daughter cells as well as in melanoma cells with intrinsic BRAFi resistance and led to dephosphorylation of EPHA2 on S897, previously demonstrated to cause inhibition of the migratory capacity. AKT and RSK, both reported to induce EPHA2 S897 phosphorylation, were also dephosphorylated after inhibition of CD13/ANPEP. FLI1 silencing also caused decreases in EPHA2 S897 phosphorylation and in total MET protein expression. In addition, silencing of FLI1 sensitized the resistant cells to BRAFi. Furthermore, we show that BRAFi in combination with the multi kinase inhibitor dasatinib can abrogate BRAFi resistance and decrease both EPHA2 S897 phosphorylation and total FLI1 protein expression. This is the first report presenting CD13/ANPEP and FLI1 as important mediators of resistance to BRAF inhibition with potential as drug targets in BRAFi refractory melanoma.
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- 2017
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16. Tissue and Serum miRNA Profile in Locally Advanced Breast Cancer (LABC) in Response to Neo-Adjuvant Chemotherapy (NAC) Treatment.
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Al-Khanbashi M, Caramuta S, Alajmi AM, Al-Haddabi I, Al-Riyami M, Lui WO, and Al-Moundhri MS
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- Adult, Breast Neoplasms drug therapy, Breast Neoplasms metabolism, Breast Neoplasms mortality, Chemotherapy, Adjuvant, Cyclophosphamide administration & dosage, Docetaxel, Doxorubicin administration & dosage, Female, Gene Expression Regulation, Neoplastic, Humans, MicroRNAs blood, Middle Aged, Neoplasm Staging, Oligonucleotide Array Sequence Analysis, Prognosis, Real-Time Polymerase Chain Reaction, Survival Rate, Taxoids administration & dosage, Trastuzumab administration & dosage, Antineoplastic Combined Chemotherapy Protocols therapeutic use, Biomarkers, Tumor genetics, Breast Neoplasms genetics, Gene Expression Profiling, MicroRNAs genetics, Neoadjuvant Therapy
- Abstract
Introduction: MicroRNAs (miRNAs) are small non-coding RNA that plays a vital role in cancer progression. Neo-adjuvant chemotherapy (NAC) has become the standard of care for locally advanced breast cancer. The aim of this study was to evaluate miRNA alterations during NAC using multiple samples of tissue and serum to correlate miRNA expression with clinico-pathological features and patient outcomes., Methods: Tissue and serum samples were collected from patients with locally advanced breast cancer undergoing NAC at four time points: time of diagnosis, after the first and fourth cycle of doxorubicin/cyclophosphamide treatment, and after the fourth cycle of docetaxel administration. First, we evaluated the miRNA expression profiles in tissue and correlated expression with clinico-pathological features. Then, a panel of four miRNAs (miR-451, miR-3200, miR-21, and miR-205) in serum samples was further validated using quantitative reverse-transcription polymerase chain reaction (RT-qPCR). The alterations in serum levels of miRNA, associations with clinical and pathological responses, correlation with clinico-pathological features, and survival outcomes were studied using Friedman, Mann-Whitney U, and Spearman, Wilcoxon signed-ranks tests. P≤0.05 was considered statistically significant., Results: We analyzed 72 tissue samples and 108 serum samples from 9 patients and 27 patients, respectively. MicroRNA expression profiling of tumor versus normal tissue revealed more than 100 differentially expressed miRNAs. Serum miR-451 levels were significantly decreased during treatment, and higher serum levels were associated with improved clinical and pathological responses and disease-free survival. This is one of the early reports on miR-3200 in response to treatment in breast cancer, as serum levels of miR-3200 found to decline during NAC, and higher serum levels were associated with lower residual breast cancer burden and relapse rates at time of diagnosis., Conclusion: Variations in serum miRNA levels during NAC treatment may be therapeutically significant for predicting response and survival outcomes.
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- 2016
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17. Whole-exome sequencing defines the mutational landscape of pheochromocytoma and identifies KMT2D as a recurrently mutated gene.
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Juhlin CC, Stenman A, Haglund F, Clark VE, Brown TC, Baranoski J, Bilguvar K, Goh G, Welander J, Svahn F, Rubinstein JC, Caramuta S, Yasuno K, Günel M, Bäckdahl M, Gimm O, Söderkvist P, Prasad ML, Korah R, Lifton RP, and Carling T
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- Adrenal Gland Neoplasms etiology, Cell Line, Tumor, Cohort Studies, DNA-Binding Proteins metabolism, Female, Gene Dosage, Humans, Male, Neoplasm Proteins metabolism, Pheochromocytoma etiology, Pheochromocytoma metabolism, Protein Isoforms genetics, Protein Isoforms metabolism, Sequence Analysis, Protein, Transcriptome, Adrenal Gland Neoplasms genetics, DNA-Binding Proteins genetics, Exome, Mutation, Neoplasm Proteins genetics, Pheochromocytoma genetics
- Abstract
As subsets of pheochromocytomas (PCCs) lack a defined molecular etiology, we sought to characterize the mutational landscape of PCCs to identify novel gene candidates involved in disease development. A discovery cohort of 15 PCCs wild type for mutations in PCC susceptibility genes underwent whole-exome sequencing, and an additional 83 PCCs served as a verification cohort for targeted sequencing of candidate mutations. A low rate of nonsilent single nucleotide variants (SNVs) was detected (6.1/sample). Somatic HRAS and EPAS1 mutations were observed in one case each, whereas the remaining 13 cases did not exhibit variants in established PCC genes. SNVs aggregated in apoptosis-related pathways, and mutations in COSMIC genes not previously reported in PCCs included ZAN, MITF, WDTC1, and CAMTA1. Two somatic mutations and one constitutional variant in the well-established cancer gene lysine (K)-specific methyltransferase 2D (KMT2D, MLL2) were discovered in one sample each, prompting KMT2D screening using focused exome-sequencing in the verification cohort. An additional 11 PCCs displayed KMT2D variants, of which two were recurrent. In total, missense KMT2D variants were found in 14 (11 somatic, two constitutional, one undetermined) of 99 PCCs (14%). Five cases displayed somatic mutations in the functional FYR/SET domains of KMT2D, constituting 36% of all KMT2D-mutated PCCs. KMT2D expression was upregulated in PCCs compared to normal adrenals, and KMT2D overexpression positively affected cell migration in a PCC cell line. We conclude that KMT2D represents a recurrently mutated gene with potential implication for PCC development., (© 2015 The Authors. Genes, Chromosomes & Cancer Published by Wiley Periodicals, Inc.)
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- 2015
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18. Extravirgin olive oil up-regulates CB₁ tumor suppressor gene in human colon cancer cells and in rat colon via epigenetic mechanisms.
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Di Francesco A, Falconi A, Di Germanio C, Micioni Di Bonaventura MV, Costa A, Caramuta S, Del Carlo M, Compagnone D, Dainese E, Cifani C, Maccarrone M, and D'Addario C
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- Animals, Caco-2 Cells, Cell Line, Cell Proliferation, Colon cytology, Colon pathology, Colonic Neoplasms pathology, Colonic Neoplasms prevention & control, DNA Methylation, Dietary Fats, Unsaturated metabolism, Dietary Fats, Unsaturated standards, Dietary Fats, Unsaturated therapeutic use, Female, Fruit chemistry, Humans, Intestinal Mucosa cytology, Intestinal Mucosa metabolism, Intestinal Mucosa pathology, Neoplasm Proteins agonists, Neoplasm Proteins genetics, Neoplasm Proteins metabolism, Olea chemistry, Olive Oil, Phenylethyl Alcohol analogs & derivatives, Phenylethyl Alcohol metabolism, Plant Extracts metabolism, Plant Oils chemistry, Plant Oils standards, Promoter Regions, Genetic, Rats, Sprague-Dawley, Receptor, Cannabinoid, CB1 chemistry, Receptor, Cannabinoid, CB1 genetics, Colon metabolism, Colonic Neoplasms metabolism, Epigenesis, Genetic, Plant Oils metabolism, Receptor, Cannabinoid, CB1 agonists, Receptor, Cannabinoid, CB1 metabolism, Up-Regulation
- Abstract
Extravirgin olive oil (EVOO) represents the typical lipid source of the Mediterranean diet, an eating habit pattern that has been associated with a significant reduction of cancer risk. Diet is the more studied environmental factor in epigenetics, and many evidences suggest dysregulation of epigenetic pathways in cancer. The aim of our study was to investigate the effects of EVOO and its phenolic compounds on endocannabinoid system (ECS) gene expression via epigenetic regulation in both human colon cancer cells (Caco-2) and rats exposed to short- and long-term dietary EVOO. We observed a selective and transient up-regulation of CNR1 gene - encoding for type 1 cannabinoid receptor (CB₁) - that was evoked by exposure of Caco-2 cells to EVOO (100 ppm), its phenolic extracts (OPE, 50 μM) or authentic hydroxytyrosol (HT, 50 μM) for 24 h. None of the other major elements of the ECS (i.e., CB₂; GPR55 and TRPV1 receptors; and NAPE-PLD, DAGL, FAAH and MAGL enzymes) was affected at any time point. The stimulatory effect of OPE and HT on CB₁ expression was inversely correlated to DNA methylation at CNR1 promoter and was associated with reduced proliferation of Caco-2 cells. Interestingly, CNR1 gene was less expressed in Caco-2 cells when compared to normal colon mucosa cells, and again this effect was associated with higher level of DNA methylation at CNR1. Moreover, in agreement with the in vitro studies, we also observed a remarkable (~4-fold) and selective increase in CB₁ expression in the colon of rats receiving dietary EVOO supplementation for 10 days. Consistently, CpG methylation of rat Cnr1 promoter, miR23a and miR-301a, previously shown to be involved in the pathogenesis of colorectal cancer and predicted to target CB₁ mRNA, was reduced after EVOO administration down to ~50% of controls. Taken together, our findings demonstrating CB₁ gene expression modulation by EVOO or its phenolic compounds via epigenetic mechanism, both in vitro and in vivo, may provide a new therapeutic avenue for treatment and/or prevention of colon cancer., (Copyright © 2015 Elsevier Inc. All rights reserved.)
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- 2015
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19. MicroRNA expression patterns associated with hyperfunctioning and non-hyperfunctioning phenotypes in adrenocortical adenomas.
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Velázquez-Fernández D, Caramuta S, Özata DM, Lu M, Höög A, Bäckdahl M, Larsson C, Lui WO, and Zedenius J
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- Adolescent, Adrenal Cortex Neoplasms metabolism, Adrenocortical Adenoma metabolism, Adult, Aged, Aged, 80 and over, Aldosterone metabolism, Cohort Studies, Female, Gene Expression Profiling, Humans, Hydrocortisone metabolism, Male, Middle Aged, Oligonucleotide Array Sequence Analysis, Reverse Transcriptase Polymerase Chain Reaction, Young Adult, Adrenal Cortex metabolism, Adrenal Cortex Neoplasms genetics, Adrenocortical Adenoma genetics, Gene Expression Regulation, Neoplastic genetics, MicroRNAs genetics
- Abstract
Background: The adrenocortical adenoma (ACA) entity includes aldosterone-producing adenoma (APA), cortisol-producing adenoma (CPA), and non-hyperfunctioning adenoma (NHFA) phenotypes. While gene mutations and mRNA expression profiles have been partly characterized, less is known about the alterations involving microRNA (miRNA) expression., Aim: To characterize miRNA expression profile in relation to the subtypes of ACAs., Subjects and Methods: miRNA expression profiles were determined in 26 ACAs (nine APAs, ten CPAs, and seven NHFAs) and four adrenal references using microarray-based screening. Significance analysis of microarrays (SAM) was carried out to identify differentially expressed miRNAs between ACA and adrenal cortices or between tumor subtypes. Selected differentially expressed miRNAs were validated in an extended series of 43 ACAs and ten adrenal references by quantitative RT-PCR., Results: An hierarchical clustering revealed separate clusters for APAs and CPAs, while the NHFAs were found spread out within the APA/CPA clusters. When NHFA was excluded, the clustering analysis showed a better separation between APA and CPA. SAM analysis identified 40 over-expressed and three under-expressed miRNAs in the adenomas as compared with adrenal references. Fourteen miRNAs were common among the three ACA subtypes. Furthermore, we found specific miRNAs associated with different tumor phenotypes., Conclusion: The results suggest that miRNA expression profiles can distinguish different subtypes of ACA, which may contribute to a deeper understanding of ACA development and potential therapeutics.
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- 2014
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20. MicroRNA expression patterns related to merkel cell polyomavirus infection in human merkel cell carcinoma.
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Xie H, Lee L, Caramuta S, Höög A, Browaldh N, Björnhagen V, Larsson C, and Lui WO
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- Adult, Aged, Aged, 80 and over, Carcinoma, Merkel Cell secondary, Carcinoma, Merkel Cell virology, Female, Gene Expression Regulation, Neoplastic, Humans, Male, Middle Aged, Skin Neoplasms pathology, Skin Neoplasms virology, Transcriptome, Young Adult, Carcinoma, Merkel Cell genetics, Merkel cell polyomavirus genetics, MicroRNAs genetics, Polyomavirus Infections genetics, Skin Neoplasms genetics, Tumor Virus Infections genetics
- Abstract
Merkel cell carcinoma (MCC) is an aggressive and lethal type of neuroendocrine skin cancer. Mutated Merkel cell polyomavirus (MCV) is commonly found in MCC, and leads to upregulation of the survivin oncogene. However, ∼20% of MCC tumors do not have detectable MCV, suggesting alternative etiologies for this tumor type. In this study, our aim was to evaluate microRNA (miRNA) expression profiles and their associations with MCV status and clinical outcomes in MCC. We showed that miRNA expression profiles were distinct between MCV-positive (MCV+) and MCV-negative (MCV-) MCCs and further validated that miR-203, miR-30a-3p, miR-769-5p, miR-34a, miR-30a-5p, and miR-375 were significantly different. We also identified a subset of miRNAs associated with tumor metastasis and MCC-specific survival. Functionally, overexpression of miR-203 was found to inhibit cell growth, induce cell cycle arrest, and regulate survivin expression in MCV- MCC cells, but not in MCV+ MCC cells. Our findings reveal a mechanism of survivin expression regulation in MCC cells, and provide insights into the role of miRNAs in MCC tumorigenesis.
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- 2014
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21. The VHL gene is epigenetically inactivated in pheochromocytomas and abdominal paragangliomas.
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Andreasson A, Kiss NB, Caramuta S, Sulaiman L, Svahn F, Bäckdahl M, Höög A, Juhlin CC, and Larsson C
- Subjects
- Abdominal Neoplasms metabolism, Adrenal Gland Neoplasms metabolism, Base Sequence, Case-Control Studies, DNA Methylation, Down-Regulation, Epigenesis, Genetic, Gene Expression Regulation, Neoplastic, Humans, Molecular Sequence Data, Paraganglioma metabolism, Pheochromocytoma metabolism, Promoter Regions, Genetic, RNA, Messenger metabolism, Von Hippel-Lindau Tumor Suppressor Protein metabolism, Abdominal Neoplasms genetics, Adrenal Gland Neoplasms genetics, Paraganglioma genetics, Pheochromocytoma genetics, Von Hippel-Lindau Tumor Suppressor Protein genetics
- Abstract
Pheochromocytoma (PCC) and abdominal paraganglioma (PGL) are neuroendocrine tumors that present with clinical symptoms related to increased catecholamine levels. About a third of the cases are associated with constitutional mutations in pre-disposing genes, of which some may also be somatically mutated in sporadic cases. However, little is known about inactivating epigenetic events through promoter methylation in these very genes. Using bisulphite pyrosequencing we assessed the methylation density of 11 PCC/PGL disease genes in 96 tumors (83 PCCs and 13 PGLs) and 34 normal adrenal references. Gene expression levels were determined by quantitative RT-PCR. Both tumors and normal adrenal samples exhibited low methylation index (MetI) in the EGLN1 (PDH2), MAX, MEN1, NF1, SDHB, SDHC, SDHD, SDHAF2 (SDH5), and TMEM127 promoters, not exceeding 10% in any of the samples investigated. Aberrant RET promoter methylation was observed in two cases only. For the VHL gene we found increased MetI in tumors as compared with normal adrenals (57% vs. 27%; P<0.001), in malignant vs. benign tumors (63% vs. 55%; P<0.05), and in PGL vs. PCC (66% vs. 55%; P<0.0005). Decreased expression of the VHL gene was observed in all tumors compared with normal adrenals (P<0.001). VHL MetI and gene expressions were inversely correlated (R = -0.359, P<0.0001). Our results show that the VHL gene promoter has increased methylation compared with normal adrenals (MetI>50%) in approximately 75% of PCCs and PGLs investigated, highlighting the role of VHL in the development of these tumors.
- Published
- 2013
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22. Clinical and functional impact of TARBP2 over-expression in adrenocortical carcinoma.
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Caramuta S, Lee L, Ozata DM, Akçakaya P, Xie H, Höög A, Zedenius J, Bäckdahl M, Larsson C, and Lui WO
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, Apoptosis drug effects, Cell Line, Tumor, DEAD-box RNA Helicases genetics, Female, Humans, Male, MicroRNAs genetics, Middle Aged, RNA, Messenger metabolism, Ribonuclease III genetics, Young Adult, Adrenal Cortex Neoplasms genetics, Adrenocortical Adenoma genetics, Adrenocortical Carcinoma genetics, RNA-Binding Proteins genetics
- Abstract
Deregulation of microRNA (miRNA) expression in adrenocortical carcinomas (ACCs) has been documented to have diagnostic, prognostic, as well as functional implications. Here, we evaluated the mRNA expression of DROSHA, DGCR8, DICER (DICER1), TARBP2, and PRKRA, the core components in the miRNA biogenesis pathway, in a cohort of 73 adrenocortical tumors (including 43 adenomas and 30 carcinomas) and nine normal adrenal cortices using a RT-qPCR approach. Our results show a significant over-expression of TARBP2, DICER, and DROSHA in the carcinomas compared with adenomas or adrenal cortices (P<0.001 for all comparisons). Using western blot and immunohistochemistry analyses, we confirmed the higher expression of TARBP2, DICER, and DROSHA at the protein level in carcinoma cases. Furthermore, we demonstrate that mRNA expression of TARBP2, but not DICER or DROSHA, is a strong molecular predictor to discriminate between adenomas and carcinomas. Functionally, we showed that inhibition of TARBP2 expression in human NCI-H295R ACC cells resulted in a decreased cell proliferation and induction of apoptosis. TARBP2 over-expression was not related to gene mutations; however, copy number gain of the TARBP2 gene was observed in 57% of the carcinomas analyzed. In addition, we identified that miR-195 and miR-497 could directly regulate TARBP2 and DICER expression in ACC cells. This is the first study to demonstrate the deregulation of miRNA-processing factors in adrenocortical tumors and to show the clinical and biological impact of TARBP2 over-expression in this tumor type.
- Published
- 2013
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- View/download PDF
23. miR-205 expression promotes cell proliferation and migration of human cervical cancer cells.
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Xie H, Zhao Y, Caramuta S, Larsson C, and Lui WO
- Subjects
- Cell Line, Tumor, Cell Proliferation, Connective Tissue Growth Factor genetics, Cysteine-Rich Protein 61 genetics, Female, Humans, Uterine Cervical Neoplasms metabolism, Cell Movement genetics, Gene Expression Regulation, Neoplastic, MicroRNAs genetics, MicroRNAs metabolism, Uterine Cervical Neoplasms genetics, Uterine Cervical Neoplasms pathology
- Abstract
MicroRNAs (miRNAs) are short non-coding RNA regulators that control gene expression mainly through post-transcriptional silencing. We previously identified miR-205 in a signature for human cervical cancer using a deep sequencing approach. In this study, we confirmed that miR-205 expression was frequently higher in human cervical cancer than their matched normal tissue samples. Functionally, we demonstrate that miR-205 promotes cell proliferation and migration in human cervical cancer cells. To further understand the biological roles of miR-205, we performed in vivo crosslinking and Argonaute 2 immunoprecipitation of miRNA ribonucleoprotein complexes followed by microarray analysis (CLIP-Chip) to identify its potential mRNA targets. Applying CLIP-Chip on gain- and loss-of-function experiments, we identified a set of transcripts as potential targets of miR-205. Several targets are functionally involved in cellular proliferation and migration. Two of them, CYR61 and CTGF, were further validated by Western blot analysis and quantification of mRNA enrichment in the Ago2 immunoprecipitates using qRT-PCR. Furthermore, both CYR61 and CTGF were downregulated in cervical cancer tissues. In summary, our findings reveal novel functional roles and targets of miR-205 in human cervical cancer, which may provide new insights about its role in cervical carcinogenesis and its potential value for clinical diagnosis.
- Published
- 2012
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24. Comprehensive re-sequencing of adrenal aldosterone producing lesions reveal three somatic mutations near the KCNJ5 potassium channel selectivity filter.
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Åkerström T, Crona J, Delgado Verdugo A, Starker LF, Cupisti K, Willenberg HS, Knoefel WT, Saeger W, Feller A, Ip J, Soon P, Anlauf M, Alesina PF, Schmid KW, Decaussin M, Levillain P, Wängberg B, Peix JL, Robinson B, Zedenius J, Bäckdahl M, Caramuta S, Iwen KA, Botling J, Stålberg P, Kraimps JL, Dralle H, Hellman P, Sidhu S, Westin G, Lehnert H, Walz MK, Åkerström G, Carling T, Choi M, Lifton RP, and Björklund P
- Subjects
- Adolescent, Adrenal Cortex Neoplasms metabolism, Adrenocortical Adenoma metabolism, Adult, Aged, Base Sequence, Cohort Studies, DNA Mutational Analysis, Female, Humans, Male, Middle Aged, Mutation Rate, Sex Characteristics, Young Adult, Adrenal Cortex Neoplasms genetics, Adrenocortical Adenoma genetics, Aldosterone biosynthesis, Mutation, Sequence Analysis
- Abstract
Background: Aldosterone producing lesions are a common cause of hypertension, but genetic alterations for tumorigenesis have been unclear. Recently, either of two recurrent somatic missense mutations (G151R or L168R) was found in the potassium channel KCNJ5 gene in aldosterone producing adenomas. These mutations alter the channel selectivity filter and result in Na(+) conductance and cell depolarization, stimulating aldosterone production and cell proliferation. Because a similar mutation occurs in a mendelian form of primary aldosteronism, these mutations appear to be sufficient for cell proliferation and aldosterone production. The prevalence and spectrum of KCNJ5 mutations in different entities of adrenocortical lesions remain to be defined., Materials and Methods: The coding region and flanking intronic segments of KCNJ5 were subjected to Sanger DNA sequencing in 351 aldosterone producing lesions, from patients with primary aldosteronism and 130 other adrenocortical lesions. The specimens had been collected from 10 different worldwide referral centers., Results: G151R or L168R somatic mutations were identified in 47% of aldosterone producing adenomas, each with similar frequency. A previously unreported somatic mutation near the selectivity filter, E145Q, was observed twice. Somatic G151R or L168R mutations were also found in 40% of aldosterone producing adenomas associated with marked hyperplasia, but not in specimens with merely unilateral hyperplasia. Mutations were absent in 130 non-aldosterone secreting lesions. KCNJ5 mutations were overrepresented in aldosterone producing adenomas from female compared to male patients (63 vs. 24%). Males with KCNJ5 mutations were significantly younger than those without (45 vs. 54, respectively; p<0.005) and their APAs with KCNJ5 mutations were larger than those without (27.1 mm vs. 17.1 mm; p<0.005)., Discussion: Either of two somatic KCNJ5 mutations are highly prevalent and specific for aldosterone producing lesions. These findings provide new insight into the pathogenesis of primary aldosteronism.
- Published
- 2012
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25. The role of microRNA deregulation in the pathogenesis of adrenocortical carcinoma.
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Özata DM, Caramuta S, Velázquez-Fernández D, Akçakaya P, Xie H, Höög A, Zedenius J, Bäckdahl M, Larsson C, and Lui WO
- Subjects
- Adrenal Cortex Neoplasms metabolism, Adrenal Cortex Neoplasms pathology, Adrenocortical Carcinoma metabolism, Adrenocortical Carcinoma pathology, Adult, Aged, Aged, 80 and over, Apoptosis Regulatory Proteins biosynthesis, Apoptosis Regulatory Proteins genetics, Cell Growth Processes genetics, Cell Line, Tumor, Female, Humans, Male, MicroRNAs biosynthesis, MicroRNAs metabolism, Middle Aged, Oligonucleotide Array Sequence Analysis, Proto-Oncogene Proteins biosynthesis, Proto-Oncogene Proteins genetics, RNA, Neoplasm chemistry, RNA, Neoplasm genetics, Reverse Transcriptase Polymerase Chain Reaction, Statistics, Nonparametric, Survival Analysis, Adrenal Cortex Neoplasms genetics, Adrenocortical Carcinoma genetics, Gene Expression Regulation, Neoplastic, MicroRNAs genetics
- Abstract
Adrenocortical carcinoma (ACC) is an aggressive tumor showing frequent metastatic spread and poor survival. Although recent genome-wide studies of ACC have contributed to our understanding of the disease, major challenges remain for both diagnostic and prognostic assessments. The aim of this study was to identify specific microRNAs (miRNAs) associated with malignancy and survival of ACC patients. miRNA expression profiles were determined in a series of ACC, adenoma, and normal cortices using microarray. A subset of miRNAs showed distinct expression patterns in the ACC compared with adrenal cortices and adenomas. Among others, miR-483-3p, miR-483-5p, miR-210, and miR-21 were found overexpressed, while miR-195, miR-497, and miR-1974 were underexpressed in ACC. Inhibition of miR-483-3p or miR-483-5p and overexpression of miR-195 or miR-497 reduced cell proliferation in human NCI-H295R ACC cells. In addition, downregulation of miR-483-3p, but not miR-483-5p, and increased expression of miR-195 or miR-497 led to significant induction of cell death. Protein expression of p53 upregulated modulator of apoptosis (PUMA), a potential target of miR-483-3p, was significantly decreased in ACC, and inversely correlated with miR-483-3p expression. In addition, high expression of miR-503, miR-1202, and miR-1275 were found significantly associated with shorter overall survival among patients with ACC (P values: 0.006, 0.005, and 0.042 respectively). In summary, we identified additional miRNAs associated with ACC, elucidated the functional role of four miRNAs in the pathogenesis of ACC cells, demonstrated the potential involvement of the pro-apoptotic factor PUMA (a miR-483-3p target) in adrenocortical tumors, and found novel miRNAs associated with survival in ACC.
- Published
- 2011
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26. miR-185 and miR-133b deregulation is associated with overall survival and metastasis in colorectal cancer.
- Author
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Akçakaya P, Ekelund S, Kolosenko I, Caramuta S, Ozata DM, Xie H, Lindforss U, Olivecrona H, and Lui WO
- Subjects
- Adult, Aged, Aged, 80 and over, Cluster Analysis, Colorectal Neoplasms mortality, Down-Regulation, Female, Gene Expression Profiling, Humans, Male, Middle Aged, Neoplasm Metastasis, Prognosis, Colorectal Neoplasms physiopathology, Gene Expression Regulation, Neoplastic, MicroRNAs genetics
- Abstract
Colorectal cancer (CRC) is one of the most common and deadly forms of cancer. Despite improved treatment modalities, post-operative recurrence and metastasis remain the major problems for extending patient survival after surgery. This highlights the need to search for biomarkers for prognostication and treatment stratification of colorectal cancer patients. In this study, we applied the SYBR-green quantitative PCR-based array approach to screen for differentially expressed miRNAs between patients with short (<50 months, range 10-33 months) and long survival (≥ 50 months, range 50-152 months). The selected candidate prognostic miRNAs were validated in a cohort of 50 CRC patients by TaqMan quantitative PCR. We found that high expression of miR-185 and low expression of miR-133b were correlated with poor survival (p=0.001 and 0.028, respectively) and metastasis (p=0.007 and 0.036, respectively) in colorectal cancer. Our findings suggest the potential prognostic values of these miRNAs for predicting clinical outcome after surgery.
- Published
- 2011
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27. MicroRNA expression profiles associated with mutational status and survival in malignant melanoma.
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Caramuta S, Egyházi S, Rodolfo M, Witten D, Hansson J, Larsson C, and Lui WO
- Subjects
- Adolescent, Adult, Aged, Aged, 80 and over, DNA Mutational Analysis, Female, Gene Expression Regulation, Neoplastic, Genes, ras genetics, Genome-Wide Association Study, Humans, Lymphatic Metastasis, Male, Melanocytes physiology, Melanoma secondary, Middle Aged, Prognosis, Proto-Oncogene Proteins B-raf genetics, Skin Neoplasms pathology, Young Adult, Gene Expression Profiling, Melanoma genetics, Melanoma mortality, MicroRNAs genetics, Skin Neoplasms genetics, Skin Neoplasms mortality
- Abstract
Malignant cutaneous melanoma is a highly aggressive form of skin cancer. Despite improvements in early melanoma diagnosis, the 5-year survival rate remains low in advanced disease. Therefore, novel biomarkers are urgently needed to devise new means of detection and treatment. In this study, we aimed to improve our understanding of microRNA (miRNA) deregulation in melanoma development and their impact on patient survival. Global miRNA expression profiles of a set of melanoma lymph node metastases, melanoma cell lines, and melanocyte cultures were determined using Agilent array. Deregulated miRNAs were evaluated in relation with clinical characteristics, patient survival, and mutational status for BRAF and NRAS. Several miRNAs were differentially expressed between melanocytes and melanomas as well as melanoma cell lines. In melanomas, miR-193a, miR-338, and miR-565 were underexpressed in cases with a BRAF mutation. Furthermore, low expression of miR-191 and high expression of miR-193b were associated with poor melanoma-specific survival. In conclusion, our findings show miRNA dysregulation in malignant melanoma and its relation to established molecular backgrounds of BRAF and NRAS oncogenic mutations. The identification of an miRNA classifier for poor survival may lead to the development of miRNA detection as a complementary prognostic tool in clinical practice.
- Published
- 2010
- Full Text
- View/download PDF
28. Multiplex protein assays based on real-time magnetic nanotag sensing.
- Author
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Osterfeld SJ, Yu H, Gaster RS, Caramuta S, Xu L, Han SJ, Hall DA, Wilson RJ, Sun S, White RL, Davis RW, Pourmand N, and Wang SX
- Subjects
- Biological Assay instrumentation, Humans, Magnetics instrumentation, Magnetics methods, Molecular Diagnostic Techniques instrumentation, Monitoring, Physiologic instrumentation, Monitoring, Physiologic methods, Nanotechnology instrumentation, Sensitivity and Specificity, Biological Assay methods, Biomarkers, Tumor analysis, Molecular Diagnostic Techniques methods, Nanotechnology methods
- Abstract
Magnetic nanotags (MNTs) are a promising alternative to fluorescent labels in biomolecular detection assays, because minute quantities of MNTs can be detected with inexpensive giant magnetoresistive (GMR) sensors, such as spin valve (SV) sensors. However, translating this promise into easy to use and multilplexed protein assays, which are highly sought after in molecular diagnostics such as cancer diagnosis and treatment monitoring, has been challenging. Here, we demonstrate multiplex protein detection of potential cancer markers at subpicomolar concentration levels and with a dynamic range of more than four decades. With the addition of nanotag amplification, the analytic sensitivity extends into the low fM concentration range. The multianalyte ability, sensitivity, scalability, and ease of use of the MNT-based protein assay technology make it a strong contender for versatile and portable molecular diagnostics in both research and clinical settings.
- Published
- 2008
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- View/download PDF
29. Suspension bead array branch migration displacement assay for rapid STR analysis.
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Villablanca A, Karhanek M, Caramuta S, Yu H, Jejelowo O, Webb CD, and Pourmand N
- Subjects
- Humans, Microspheres, Nucleic Acid Hybridization methods, Oligonucleotide Probes, Polymerase Chain Reaction methods, Sensitivity and Specificity, Spectrometry, Fluorescence methods, Suspensions, Microsatellite Repeats, Oligonucleotide Array Sequence Analysis methods
- Abstract
STR analysis is commonly used in forensic and genetic studies. STRs are currently discriminated based on size, primarily by gel- and column-based approaches. Hybridization-based approaches have the potential to allow high-throughput analysis of STRs; however, development of such approaches has been limited by the difficulty in discriminating between STRs of similar length. We have recently described several innovations to enable STR analysis using an array-based hybridization approach for high- throughput STR analysis. Here we extend that approach by incorporating the array into microspheres and adding a discriminatory branch migration displacement step. This microsphere-based platform uses Luminex xMAP technology and improves the sensitivity, selectivity, and speed of the assay. We demonstrate the feasibility, speed, and reliability of the assay for STR detection by correctly analyzing two STR loci in 20 forensic DNA samples of known STR type. The multiplex, bead-based approach provides a high-throughput and more portable STR analysis.
- Published
- 2008
- Full Text
- View/download PDF
30. Molecular and cytogenetic subgroups of oropharyngeal squamous cell carcinoma.
- Author
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Perrone F, Suardi S, Pastore E, Casieri P, Orsenigo M, Caramuta S, Dagrada G, Losa M, Licitra L, Bossi P, Staurengo S, Oggionni M, Locati L, Cantu G, Squadrelli M, Carbone A, Pierotti MA, and Pilotti S
- Subjects
- Biomarkers, Tumor analysis, Carcinoma, Squamous Cell virology, Cell Cycle Proteins physiology, Chromosome Aberrations, Chromosomes, Human, Pair 9, Cyclin D1 metabolism, Cyclin-Dependent Kinase 4 metabolism, ErbB Receptors metabolism, Genes, Tumor Suppressor physiology, Human papillomavirus 16 isolation & purification, Human papillomavirus 16 metabolism, Humans, Oropharyngeal Neoplasms virology, Proto-Oncogene Proteins B-raf metabolism, Carcinoma, Squamous Cell classification, Carcinoma, Squamous Cell genetics, Cytogenetic Analysis, Oropharyngeal Neoplasms classification, Oropharyngeal Neoplasms genetics
- Abstract
Purpose: The aim of this study was to acquire further insights into the pathogenetic pathways of head and neck squamous cell carcinomas (HNSCC) that may be useful for identifying new biomarkers instrumental in developing more specific treatment approaches., Experimental Design: Cell cycle regulators and epidermal growth factor receptor (EGFR) and BRAF genes were analyzed in a series of 90 oropharyngeal SCCs of a cohort of surgically treated patients from a single institution, and the results were matched with the presence of high-risk human papillomavirus (HR-HPV) DNA and the TP53 status., Results: At least four distinct groups of tumors were identified sharing a common histology but displaying different molecular/cytogenetic patterns: (a) 19% were HPV-positive SCCs whose lack of alterations of the investigated genes could explain their particular natural history, which requires less aggressive treatment; (b) 37% were HPV-negative SCCs carrying TP53 mutations, which may be more effectively treated by drugs acting through p53-independent apoptosis; (c) 34% were HPV-negative SCCs carrying wild-type TP53 and loss of 9p21 (p16INK4a and p15INK4b) and/or cyclin D1 overexpression that justify treatment with DNA-damaging drugs followed by cell cycle inhibitors; and (d) 10% were HPV-negative lacking tumor suppressor genes and cell cycle alterations. The second, third, and fourth groups also showed an increased copy number of EGFR and chromosome 7 (43%) that might justify the additional or alternative use of EGFR inhibitors., Conclusions: Our findings suggest that assessing HPV, TP53, 9p21, and EGFR status may be crucial to finding more tailored and beneficial treatments for oropharyngeal SCCs.
- Published
- 2006
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- View/download PDF
31. Regulation of lipocalin-2 gene by the cancer chemopreventive retinoid 4-HPR.
- Author
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Caramuta S, De Cecco L, Reid JF, Zannini L, Gariboldi M, Kjeldsen L, Pierotti MA, and Delia D
- Subjects
- Acute-Phase Proteins metabolism, Cell Line, Tumor, Cell Survival drug effects, Cytosol drug effects, Cytosol metabolism, Down-Regulation drug effects, Free Radicals metabolism, Gene Expression Regulation, Neoplastic drug effects, Humans, Lipocalin-2, Lipocalins, Neoplasms metabolism, Neoplasms pathology, Proto-Oncogene Proteins metabolism, RNA, Small Interfering genetics, Up-Regulation, Acute-Phase Proteins genetics, Antineoplastic Agents pharmacology, Fenretinide pharmacology, Neoplasms genetics, Proto-Oncogene Proteins genetics
- Abstract
N-(4-Hydroxyphenyl)retinamide (4-HPR) is a nonclassical retinoid with cancer preventive effects in vivo and antiproliferative and apoptotic activities in vitro. Examining the transcriptional profile of human breast cancer cell lines, MCF7 and T47D, treated with 4-HPR, we identified the lipocalin member LCN2 (NGAL or 24p3) as a gene, markedly induced by the retinoid. Because of its presumed function in apoptosis, LCN2 was examined more thoroughly in response to 4-HPR. Like mRNA, the expression of LCN2 protein in MCF7 and T47D cells was highly induced in a time-dependent manner by 4-HPR, but not by its inactive metabolite 4-MPR and, to some extent, this event was linked to the free radicals normally generated by 4-HPR. All-trans retinoic acid also induced LCN2 protein, particularly in T47D cells. Ectopic LCN2 compromised cell viability, and the few MCF7 clones that survived LCN2 overexpression were less sensitive than do mock cells to 4HPR, indicating that selective pressure for survival to LCN2 confers cross-resistance to 4-HPR. Significantly, ablation of LCN2 induction by siRNA did not modify the response to 4-HPR, implying that LCN2 is not critical for apoptosis by 4-HPR. Our results indicate that 4-HPR markedly induces LCN2 expression, but this event may not represent an apoptotic response., (Copyright 2006 Wiley-Liss, Inc.)
- Published
- 2006
- Full Text
- View/download PDF
32. Phenotype-genotype correlation: challenge of intestinal-type adenocarcinoma of the nasal cavity and paranasal sinuses.
- Author
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Frattini M, Perrone F, Suardi S, Balestra D, Caramuta S, Colombo F, Licitra L, Cantù G, Pierotti MA, and Pilotti S
- Subjects
- Adaptor Proteins, Signal Transducing, Adenomatous Polyposis Coli Protein genetics, Carrier Proteins genetics, Chromosomes, Human, Pair 18 genetics, Colorectal Neoplasms genetics, DNA Mismatch Repair, Gene Expression Regulation, Neoplastic, Genes, ras genetics, Genotype, Humans, Loss of Heterozygosity, MutL Protein Homolog 1, MutS Homolog 2 Protein genetics, Mutation, Nuclear Proteins genetics, Phenotype, Proto-Oncogene Proteins B-raf genetics, beta Catenin genetics, Adenocarcinoma genetics, Nasal Cavity, Nose Neoplasms genetics, Paranasal Sinus Neoplasms genetics
- Abstract
Background: Intestinal-type adenocarcinoma (ITAC) of the nasal cavity and paranasal sinuses shows microscopic features indistinguishable from colorectal cancer. Our aim was to verify whether the morphologic resemblances mirror genetic profile similarities., Methods: Twenty consecutive surgically treated ITAC cases, previously investigated for p16(INK4a) and TP53, were investigated for hMLH1, hMSH2, and beta-catenin immunoreactivity, and for adenomatous polyposis coli (APC), K-ras, and BRAF gene mutations., Results: One case was immunonegative for both hMLH1 and hMSH2, and 12 tumors (40%) revealed a strong beta-catenin overexpression. No BRAF and APC truncating mutations were identified, whereas K-ras mutations were detected in 9 ITACs (50%)., Conclusions: Our data confirm the phenotypic similarities at the genetic level between colorectal cancer and ITACs showing deregulation of K-Ras/BRAF and loss of heterozygosity (LOH) of chromosome 18q. By contrast, both frequency rate and type of inactivation of the APC-beta-catenin pathway differ in the 2 tumors, suggesting different gatekeeper events in the early development of ITAC (p16(INK4a) and TP53) and colorectal cancer (APC)., ((c) 2006 Wiley Periodicals, Inc.)
- Published
- 2006
- Full Text
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33. 9p21 locus analysis in high-risk gastrointestinal stromal tumors characterized for c-kit and platelet-derived growth factor receptor alpha gene alterations.
- Author
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Perrone F, Tamborini E, Dagrada GP, Colombo F, Bonadiman L, Albertini V, Lagonigro MS, Gabanti E, Caramuta S, Greco A, Torre GD, Gronchi A, Pierotti MA, and Pilotti S
- Subjects
- Adult, Aged, Cell Cycle Proteins genetics, Chromosome Deletion, Cyclin-Dependent Kinase Inhibitor p15, Cyclin-Dependent Kinase Inhibitor p16 genetics, DNA Methylation, Female, Humans, Male, Middle Aged, Mutation, Phosphorylation, Promoter Regions, Genetic, Tumor Suppressor Protein p14ARF genetics, Tumor Suppressor Proteins genetics, Chromosomes, Human, Pair 9, Gastrointestinal Stromal Tumors genetics, Proto-Oncogene Proteins c-kit genetics, Receptor, Platelet-Derived Growth Factor alpha genetics
- Abstract
Background: Gastrointestinal stromal tumors (GISTs) are noncomplex sarcomas that often are due to c-kit-activating and platelet-derived growth factor receptor alpha gene (PDGFRalpha)-activating mutations and perturbations of their related signaling pathways. Molecular and cytogenetic findings have indicated correlations between tumor progression and high-risk GISTs with c-kit mutations, the overexpression of genes such as ezrin, and losses at 9p. In particular, it was reported recently that malignant GISTs showed alterations in the p16INK4a gene located at the 9p21 locus., Methods: To assess the involvement of p14ARF and p15INK4b in addition to p16INK4a in GISTs, the authors undertook a molecular and cytogenetic study of the 9p21 locus. A series of 22 pre-Gleevec era, cryopreserved, high-risk GISTs that were characterized well in terms of KIT and PDGFRalpha receptors were investigated for mRNA expression, homozygous deletions, mutations, and promoter methylation of locus 9p21, in some instances complemented by fluorescent in situ hybridization studies., Results: The results indicated the loss of p16INK4a mRNA expression in 41% of the GISTs, mainly due to the homozygous deletion of both the p16INK4a gene and the p14ARF gene (24%). No mutations were found, and promoter methylation (detected by means of methylation-specific polymerase chain reaction analysis in 27% of tumors) was restricted mainly to the p15INK4b gene (20%). It is noteworthy that, in all of the methylated GISTs, the epigenetic promoter alteration was coupled with mRNA expression., Conclusions: Alterations in the 9p21 locus were found cumulatively in 54% of the tumors in the current series and were represented mainly by the loss of tumor suppressor gene expression. The p16INK4a deletion, which always was coupled with p14ARF gene loss, seemed to be the most common 9p21 inactivation mechanism.
- Published
- 2005
- Full Text
- View/download PDF
34. Gene expression profiling of advanced ovarian cancer: characterization of a molecular signature involving fibroblast growth factor 2.
- Author
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De Cecco L, Marchionni L, Gariboldi M, Reid JF, Lagonigro MS, Caramuta S, Ferrario C, Bussani E, Mezzanzanica D, Turatti F, Delia D, Daidone MG, Oggionni M, Bertuletti N, Ditto A, Raspagliesi F, Pilotti S, Pierotti MA, Canevari S, and Schneider C
- Subjects
- Cell Line, Tumor, Extracellular Matrix Proteins genetics, Female, Humans, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Receptors, Fibroblast Growth Factor physiology, Fibroblast Growth Factor 2 physiology, Gene Expression Profiling, Ovarian Neoplasms genetics
- Abstract
Epithelial ovarian cancer (EOC) is the gynecological disease with the highest death rate. We applied an automatic class discovery procedure based on gene expression profiling to stages III-IV tumors to search for molecular signatures associated with the biological properties and progression of EOC. Using a complementary DNA microarray containing 4451 cancer-related, sequence-verified features, we identified a subset of EOC characterized by the expression of numerous genes related to the extracellular matrix (ECM) and its remodeling, along with elements of the fibroblast growth factor 2 (FGF2) signaling pathway. A total of 10 genes were validated by quantitative real-time polymerase chain reaction, and coexpression of FGF2 and fibroblast growth factor receptor 4 in tumor cells was revealed by immunohistochemistry, confirming the reliability of gene expression by cDNA microarray. Since the functional relationships among these genes clearly suggested involvement of the identified molecular signature in processes related to epithelial-stromal interactions and/or epithelial-mesenchymal cellular plasticity, we applied supervised learning analysis on ovarian-derived cell lines showing distinct cellular phenotypes in culture. This procedure enabled construction of a gene classifier able to discriminate mesenchymal-like from epithelial-like cells. Genes overexpressed in mesenchymal-like cells proved to match the FGF2 signaling and ECM molecular signature, as identified by unsupervised class discovery on advanced tumor samples. In vitro functional analysis of the cell plasticity classifier was carried out using two isogenic and immortalized cell lines derived from ovarian surface epithelium and displaying mesenchymal and epithelial morphology, respectively. The results indicated the autocrine, but not intracrine stimulation of mesenchymal conversion and cohort/scatter migration of cells by FGF2, suggesting a central role for FGF2 signaling in the maintenance of cellular plasticity of ovary-derived cells throughout the carcinogenesis process. These findings raise mechanistic hypotheses on EOC pathogenesis and progression that might provide a rational underpinning for new therapeutic modalities.
- Published
- 2004
- Full Text
- View/download PDF
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