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Palermo M, D'Elia C, Trenti E, Comploj E, Mian C, Schwienbacher C, Heidegger I, Clauser S, Pycha A, Vjaters E. Prospective evaluation of the RT-PCR based urinary marker Bladder Epicheck® as a diagnostic tool in upper urinary tract tumor. Minerva Urol Nephrol 2024; 76:195-202. [PMID: 38498297 DOI: 10.23736/s2724-6051.23.05488-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/20/2024]
Abstract
BACKGROUND Upper-tract-urothelial-carcinoma (UTUC) represents 5-10% of all urothelial-neoplasms with increasing incidence in the last decades. Current standard tools for diagnosis of UTUC include cytology, computed tomography (CT) urography and ureterorenoscopy (URS). The aim of this study was to evaluate the impact of Bladder Epicheck® Test as diagnostic tool for UTUC diagnosis and recurrence. METHODS Overall, 136 urine samples, selective collected from upper-urinary-tract before URS for suspicion of UTUC were analyzed with cytology and Bladder Epicheck® Test. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of both markers were calculated and compared to URS and/or histology as reference. RESULTS UTUC was detected in 40 cases (33.3%), among them 30 were classified as low-grade (LG) and 10 as high-grade (HG). Overall sensitivity of Bladder Epicheck® for UTUC detection was 65% compared to 42.5% for cytology, increasing to 100% for Bladder Epicheck® and 90% for cytology if considering only HG tumors. Overall specificity of Bladder Epicheck® was 81.2% and of cytology 93.7%. PPV and NPV were 63.4% and 82.2% for Bladder Epicheck® and 77.2% and 76.5% for cytology. Considering an EpiScore cut-off >75, instead of 60, specificity of Bladder Epicheck® improves to 89% and PPV to 74.2%. Limitations include the use of a marker validated only for bladder-cancer and the relatively small number of cases. CONCLUSIONS Due to its high sensitivity for HG tumors, the Bladder Epicheck® Test can be used in diagnosis and treatment decision-making of UTUC. Furthermore, it could be very useful in follow-up of UTUC, after endoscopic treatment to postpone or avoid unnecessary endoscopic exploration. Even if further studies are needed to validate these findings, Bladder Epicheck® could be a promising clinical tool for detection of UTUC.
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Affiliation(s)
| | - Carolina D'Elia
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy
| | - Emanuela Trenti
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy -
| | - Evi Comploj
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy
| | - Christine Mian
- Department of Pathology, Central Hospital of Bolzano, Bolzano, Italy
| | | | - Isabel Heidegger
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Silvia Clauser
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy
| | - Armin Pycha
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy
- Medical School, Sigmund Freud Private University, Vienna, Austria
| | - Egils Vjaters
- Department of Urology, Riga Stradins University Hospital, Riga, Latvia
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Pycha S, D'Elia C, Mian C, Schwienbacher C, Hanspeter E, Palermo M, Pycha A, Danuser H, Trenti E. Evaluation of the M371-Test Under Real-life Conditions for Diagnosis and Follow Up of Testicular Germ Cell Tumors. Anticancer Res 2023; 43:1649-1653. [PMID: 36974797 DOI: 10.21873/anticanres.16316] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Revised: 12/23/2022] [Accepted: 12/28/2022] [Indexed: 03/29/2023]
Abstract
BACKGROUND/AIM The aim of the study was to establish the performance of the M371-Test on the Thermocycler Rotor-GeneQ (Qiagen) platform for diagnosis and follow-up of testicular tumors and to evaluate the test under real-life conditions in comparison to the classical markers alpha-fetoprotein (AFP), beta-human chorionic gonadotropin (β-HCG) and lactate dehydrogenase (LDH). PATIENTS AND METHODS Forty-four patients, of median age 29 years (range=24-84) were included in this prospective study at our institution between March 2021 and September 2022. Of the 44 patients, 23 had a suspicion of testicular cancer (TC) and 21 were under follow-up for TC. In total, 96 M371-Tests were performed and compared with AFP, β-HCG, LDH using histological diagnosis and/or computer tomography (CT) scan as the gold standard. RESULTS In the patients with suspicion of TC, the M371-Test showed a sensitivity of 73.7%, AFP of 21%, LDH of 31.6% and β-HCG of 42.1%. In the patients under follow-up for TC, the M371-Test showed a sensitivity of 86.4%, AFP of 50%, LDH of 31.8% and β-HCG of 63.6%. In germ cell tumours (GCT)/non-seminomas, M371-Test had a sensitivity of 83.3%, AFP of 77.8%, LDH of 38.9% and β-HCG of 66.7%. In GCT/seminomas, M371-Test had a sensitivity of 85%, AFP of 5%, LDH of 30% and β-HCG of 50%. CONCLUSION Under real life conditions performed on the real-time Thermocycler Rotor-GeneQ (Qiagen) platform, the M371-Test shows an outstanding performance and is far beyond the sensitivity of the classical markers for detecting GCTs and in the follow-up of patients after GCT, especially in seminomas.
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Affiliation(s)
- Stefan Pycha
- Faculty of Medicine, University of Bern, Bern, Switzerland
| | - Carolina D'Elia
- Department of Urology, Provincial Hospital of Bolzano, Bolzano, Italy
| | - Christine Mian
- Department of Pathology, Provincial Hospital of Bolzano, Bolzano, Italy
| | | | - Esther Hanspeter
- Department of Pathology, Provincial Hospital of Bolzano, Bolzano, Italy
| | | | - Armin Pycha
- Department of Urology, Provincial Hospital of Bolzano, Bolzano, Italy
- Sigmund Freud Private University, Vienna, Austria
| | | | - Emanuela Trenti
- Department of Urology, Provincial Hospital of Bolzano, Bolzano, Italy;
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Pycha S, Trenti E, Mian C, Schwienbacher C, Hanspeter E, Palermo M, Pycha A, Danuser H, D'Elia C. Diagnostic value of Xpert® BC Detection, Bladder Epicheck®, Urovysion® FISH and cytology in the detection of upper urinary tract urothelial carcinoma. World J Urol 2023; 41:1323-1328. [PMID: 36929411 DOI: 10.1007/s00345-023-04350-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2022] [Accepted: 02/26/2023] [Indexed: 03/18/2023] Open
Abstract
PURPOSE Following the current guidelines, diagnosis and staging for upper urinary tract tumours (UTUC) can be performed with Computed Tomography, urography, ureterorenoscopy (URS) and selective cytology. The aim of the study was to evaluate the performance of the Xpert®-BC-Detection and the Bladder-Epicheck®-test in the detection of UTUC and compare it with cytology and the Urovysion®-FISH test using histology and URS as gold standard. METHODS A total of 97 analyses were collected through selective catheterization of the ureter before URS to test for cytology, Xpert®-BC-Detection, Bladder-Epicheck® and Urovysion®-FISH. Sensitivity, specificity, and predictive values were calculated using histology results/URS as reference. RESULTS Overall sensitivity was 100% for Xpert®-BC-Detection, 41.9% for cytology, 64.5% for Bladder-Epicheck® and 87.1% for Urovysion®-FISH. The sensitivity of Xpert®-BC-Detection was 100% in both, LG and HG tumours, sensitivity of cytology increased from 30.8% in LG to 100% in HG, for Bladder-Epicheck® from 57.7% in LG to 100% in HG and of Urovysion®-FISH from 84.6% in LG to 100% in HG tumours. Specificity was 4.5% for Xpert®-BC-Detection, 93.9% for cytology, 78.8% for Bladder-Epicheck® and 81.8% for Urovysion®-FISH. PPV was 33% for Xpert®-BC-Detection, 76.5% for cytology, 58.8% for Bladder-Epicheck® and 69.2% for Urovysion®FISH. NPV was 100% for Xpert®-BC-Detection, 77.5% for cytology, 82.5% for Bladder-Epicheck® and 93.1% for Urovysion®FISH. CONCLUSION Bladder-Epicheck® and Urovysion®FISH along with cytology could be a helpful ancillary method in the diagnosis and follow-up of UTUC while due to its low specificity Xpert®-BC Detection seems to be of limited usefulness.
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Affiliation(s)
- Stefan Pycha
- University of Bern, Faculty of Medicine, Bern, Switzerland
| | - Emanuela Trenti
- Department of Urology, Provincial Hospital of Bolzano, Lorenz Böhler St 5, 39100, Bolzano, Italy.
| | - Christine Mian
- Department of Pathology, Provincial Hospital of Bolzano, Bolzano, Italy
| | | | - Esther Hanspeter
- Department of Pathology, Provincial Hospital of Bolzano, Bolzano, Italy
| | | | - Armin Pycha
- Department of Urology, Provincial Hospital of Bolzano, Lorenz Böhler St 5, 39100, Bolzano, Italy.,Sigmund Freud Private University, Vienna, Austria
| | | | - Carolina D'Elia
- Department of Urology, Provincial Hospital of Bolzano, Lorenz Böhler St 5, 39100, Bolzano, Italy
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D’Elia C, Pycha S, Mian C, Schwienbacher C, Hanspeter E, Palermo M, Pycha A, Danuser H, Trenti E. Evaluation of the M371 test under real life conditions for the diagnosis and follow up of testicular germ cell tumours. Eur Urol 2023. [DOI: 10.1016/s0302-2838(23)00792-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/12/2023]
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D’Elia C, Trenti E, Krause P, Pycha A, Mian C, Schwienbacher C, Hanspeter E, Kafka M, Palermo M, Spedicato GA, Holl S, Pycha A. Xpert® bladder cancer detection as a diagnostic tool in upper urinary tract urothelial carcinoma: preliminary results. Ther Adv Urol 2022; 14:17562872221090320. [PMID: 35450126 PMCID: PMC9016582 DOI: 10.1177/17562872221090320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2021] [Accepted: 03/10/2022] [Indexed: 11/15/2022] Open
Abstract
Objectives: Upper urinary tract urothelial carcinoma (UTUC) represents about 5–10% of all
urothelial malignancies with an increasing incidence. The standard
diagnostic tools for the detection of UTUC are cytology, computed tomography
(CT) urography, and ureterorenoscopy (URS). No biomarker to be included in
the daily clinical practice has yet been identified. The aim of our study
was to evaluate the potential role of Xpert® Bladder-Cancer (BC)-Detection
in the diagnosis of UTUC. Methods: Eighty-two patients underwent 111 URS with Xpert® BC-Detection, cytology, or
Urovysion® analysis of UT for suspicion of UTUC. Twenty-four cases were
excluded from the analysis due to a non-diagnostic Xpert® BC-Detection,
cytology, or Urovysion®. Samples were analyzed with upper tract (UT) urinary
cytology, with Xpert® BC-Detection on UT urines, and with Urovysion®
Fluorescence in situ hybridization (FISH) test. After urine
collection, the patients underwent retrograde pyelography and/or URS, and if
positive a UT biopsy. The Xpert® BC-Detection was reported by the software
as negative or positive [cut-off total Linear Discriminant Analysis (LDA) =
0.45]. Sensitivity, specificity, positive predictive value (PPV), and
negative predictive value (NPV) of cytology, Xpert® BC-Detection and
Urovysion-FISH were calculated using URS and/or histology results as
reference. Results: In all, 27 (31%) of 87 URS resulted positive, with 20 low-grade (LG) and 7
high-grade (HG) tumors. Overall sensitivity was 51.9% for cytology, 100% for
Xpert® BC-Detection, and 92.6% for Urovysion. The sensitivity of cytology
increased from 26% in LG to 100% in HG tumors. For Xpert® BC-Detection,
sensitivity was 100% both in LG and in HG, and for Urovysion-FISH, it
increased from 90% in LG to 100% in HG tumors. PPV was 82.4% for cytology,
35% for Xpert® BC-Detection, and 73.5% for Urovysion. NPV was 81.4% for
cytology, 100% for Xpert® BC-Detection, and 96.2% for Urovysion. Conclusion: The excellent NPV of Xpert® BC-Detection allows to avoid unnecessary
endoscopic exploration of the UT, reducing invasiveness and URS
complications in the follow-up of UTUC.
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Affiliation(s)
- Carolina D’Elia
- Department of Urology, Provincial Hospital of Bolzano, Bolzano, Italy
| | - Emanuela Trenti
- Department of Urology, Bolzano Provincial Hospital, Lorenz Böhler St 5, Bolzano 39100, Italy
| | - Philipp Krause
- Department of Urology, Provincial Hospital of Bolzano, Bolzano, Italy
| | | | - Christine Mian
- Department of Pathology, Provincial Hospital of Bolzano, Bolzano, Italy
| | | | - Esther Hanspeter
- Department of Pathology, Provincial Hospital of Bolzano, Bolzano, Italy
| | - Mona Kafka
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | | | | | - Stefanie Holl
- Medical School, Sigmund Freud Private University, Vienna, Austria
| | - Armin Pycha
- Department of Urology, Provincial Hospital of Bolzano, Bolzano, Italy Medical School, Sigmund Freud Private University, Vienna, Austria
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D'Elia C, Trenti E, Krause P, Pycha A, Mian C, Schwienbacher C, Hanspeter E, Kafka M, Palermo M, Spedicato G, Holl S, Pycha A. Xpert® bc detection as a diagnostic tool in upper urinary tract urothelial carcinoma: Preliminary results. Eur Urol 2022. [DOI: 10.1016/s0302-2838(22)00374-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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König E, Nicoletti A, Pattaro C, Annesi G, Melotti R, Gialluisi A, Schwienbacher C, Picard A, Blankenburg H, Pichler I, Modugno N, Ciullo M, Esposito T, Domingues FS, Hicks AA, Zappia M, Pramstaller PP. Exome-wide association study of levodopa-induced dyskinesia in Parkinson's disease. Sci Rep 2021; 11:19582. [PMID: 34599261 PMCID: PMC8486836 DOI: 10.1038/s41598-021-99393-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Accepted: 09/16/2021] [Indexed: 11/09/2022] Open
Abstract
Levodopa is the standard long-term dopamine replacement therapy to treat Parkinson's disease (PD) symptoms. With time, levodopa may induce debilitating dyskinesias (LID), the treatment of which represents a large clinically unmet need. However, time-to-LID onset varies between patients, reflecting a possible genetic component. We performed an hypothesis-free whole-exome sequencing (WES)-based screening of time-to-LID onset and attempted replication of previously published candidate gene studies. A WES association analysis was carried out in 134 PD patients in a meta-analytical framework. Replication was attempted in an independent study of 97 PD patients. Variants from previously reported candidate genes (OPRM1, COMT, BDNF) were also specifically examined. We significantly replicated, for the first time, an association of variant rs1799971 in the OPRM1 gene with time-to-LID onset. Furthermore, we identified two novel potentially functional variants, in the MAD2L2 (rs2233019) and MAP7 (rs35350783) genes, which were significantly associated at the discovery stage. In the replication study, the two variants showed direction-consistent effects but did not achieve the replication significance threshold. Our study provides the first WES results for time-to-LID onset, where we replicate association at OPRM1, and suggest new variants in MAD2L2 and MAP7 genes that are significant in discovery, but require larger datasets for replication. The results are being made publicly available to allow for independent external validation.
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Affiliation(s)
- Eva König
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Alessandra Nicoletti
- Section of Neurosciences, Department G.F. Ingrassia, University of Catania, Catania, Italy
| | - Cristian Pattaro
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Grazia Annesi
- Institute for Biomedical Research and Innovation, National Research Council, Mangone (Cosenza), Italy
| | - Roberto Melotti
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | | | - Christine Schwienbacher
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Anne Picard
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Hagen Blankenburg
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Nicola Modugno
- Mediterranean Neurological Institute (MNI), IRCCS Neuromed, Pozzilli, Italy
| | - Marina Ciullo
- Mediterranean Neurological Institute (MNI), IRCCS Neuromed, Pozzilli, Italy.,Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, Naples, Italy
| | - Teresa Esposito
- Mediterranean Neurological Institute (MNI), IRCCS Neuromed, Pozzilli, Italy.,Institute of Genetics and Biophysics "Adriano Buzzati-Traverso", National Research Council, Naples, Italy
| | - Francisco S Domingues
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy.
| | - Mario Zappia
- Section of Neurosciences, Department G.F. Ingrassia, University of Catania, Catania, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Via Luigi Galvani 31, 39100, Bozen/Bolzano, Italy
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D’Elia C, Trenti E, Folchini D, Pycha S, Mian C, Schwienbacher C, Hanspeter E, Pycha A. Xpert® bladder cancer monitor and bladder epicheck® in the follow up of patients affected by intermediate risk non muscle invasive bladder cancer (nmibc): Preliminary data. Eur Urol 2021. [DOI: 10.1016/s0302-2838(21)01098-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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D'Elia C, Folchini DM, Mian C, Hanspeter E, Schwienbacher C, Spedicato GA, Pycha S, Vjaters E, Degener S, Kafka M, Pycha A, Trenti E. Diagnostic value of Xpert ® Bladder Cancer Monitor in the follow-up of patients affected by non-muscle invasive bladder cancer: an update. Ther Adv Urol 2021; 13:1756287221997183. [PMID: 33747133 PMCID: PMC7940738 DOI: 10.1177/1756287221997183] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 01/27/2021] [Indexed: 11/18/2022] Open
Abstract
Aims: Xpert® Bladder Cancer Monitor is a urinary marker based on the evaluation of five target mRNAs overexpressed in patients with bladder cancer (BC). The aim of our study is to update our results regarding the diagnostic accuracy of the Xpert® Bladder Cancer Monitor test in the follow-up of patients with non-muscle invasive bladder cancer (NMIBC). Methods: We conducted a prospective study on 1015 samples of 416 patients (mean age 72.2 ± 10.3 years) under follow-up for NMIBC. Patients underwent voided urinary cytology, the Xpert® Bladder Cancer Monitor test and cystoscopy and, if positive, a transurethral resection of the bladder. Xpert® Bladder Cancer Monitor was reported as negative or positive: cut-off total Linear Discriminant Analysis (LDA) = 0.5. Results: We identified 168 recurrent tumours: 126 (75%) were low-grade (LG) and 42 (25%) high-grade (HG). Overall sensitivity was 17.9% for cytology, 52.4% for Xpert® Bladder Cancer Monitor and 54.2% for the two tests combined. The sensitivity of cytology increased from 6.3% in LG to 52.4% in HG tumours whereas Xpert® Bladder Cancer Monitor showed a sensitivity ranging from 42.9% in LG to 80.9% in HG tumours. Combined cytology and Xpert® Bladder Cancer Monitor yielded an overall sensitivity of 45.2% for LG and 80.9% for HG tumours. Overall specificity was 98.5% for cytology and 78.4% for Xpert® Bladder Cancer Monitor and 78.2% for the two tests combined. The area under the curve (AUC) for Xpert® Bladder Cancer Monitor was 0.71; stratifying the patients according to the European Association of Urology risk groups, the AUC was 0.69, 0.67 and 0.85 for low, intermediate and high risk, respectively (p = 0.0003). Conclusion: Our data confirm a significantly higher sensitivity of Xpert® Bladder Cancer Monitor than for cytology in a larger patient cohort. The test performed very well in terms of specificity but could not reach the high value of cytology. Along with voided urinary cytology the test could allow to reduce cystoscopies in follow-up patients, reducing discomfort to the patients and costs.
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Affiliation(s)
| | | | - Christine Mian
- Department of Pathology, Hospital of Bolzano, Bolzano, Italy
| | | | | | | | - Stefan Pycha
- Department of Urology, Riga Stradins University Hospital, Riga, Latvia
| | - Egils Vjaters
- Department of Urology, Riga Stradins University Hospital, Riga, Latvia
| | - Stephan Degener
- Department of Urology, Helios-Klinikum Wuppertal, Witten Herdecke University, Wuppertal, Germany
| | - Mona Kafka
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Armin Pycha
- Department of Urology, Hospital of Bolzano, Bolzano, Italy
| | - Emanuela Trenti
- Department of Urology, Bolzano General Hospital, Lorenz Böhler St 5, Bolzano, 39100, Italy
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D’Elia C, Trenti E, Folchini D, Pycha S, Mian C, Schwienbacher C, Hanspeter E, Pycha A. Xpert® BC detection as a diagnostic tool in upper urinary tract urothelial carcinoma: Preliminary results. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)34082-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022] Open
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D’Elia C, Trenti E, Folchini D, Pycha S, Mian C, Schwienbacher C, Hanspeter E, Pycha A. Xpert® bladder cancer monitor in the follow up of patients affected by non muscle invasive bladder cancer (NMIBC): An update. EUR UROL SUPPL 2020. [DOI: 10.1016/s2666-1683(20)33500-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022] Open
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Trenti E, Pycha S, Mian C, Schwienbacher C, Hanspeter E, Kafka M, Spedicato GA, Vjaters E, Degener S, Pycha A, D'Elia C. Comparison of 2 new real-time polymerase chain reaction-based urinary markers in the follow-up of patients with non-muscle-invasive bladder cancer. Cancer Cytopathol 2020; 128:341-347. [PMID: 31977131 DOI: 10.1002/cncy.22246] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Revised: 12/01/2019] [Accepted: 01/02/2020] [Indexed: 12/27/2022]
Abstract
BACKGROUND The objective of the current study was to compare the diagnostic accuracy of 2 new real-time polymerase chain reaction-based urinary markers with each other and with urinary cytology, cystoscopy, and/or histology in patients being followed for non-muscle-invasive bladder cancer. METHODS A total of 487 patients were enrolled in the study. Patients were evaluated using voided urine cytology, the Xpert Bladder Cancer Monitor, the Bladder EpiCheck test, and white light cystoscopy. RESULTS The overall sensitivity was 27.17% for cytology, 64.13% for the Bladder EpiCheck test, and 66.3% for the Xpert Bladder Cancer Monitor. The overall specificity was 98.82% for cytology, 82.06% for the Bladder EpiCheck test, and 76.47% for the Xpert Bladder Cancer Monitor. The negative predictive value was very similar for the 3 tests at 83.56% for cytology, 89.42% for the Bladder EpiCheck test, and 89.35% for the Xpert Bladder Cancer Monitor. When combined, the Bladder EpiCheck test and Xpert Bladder Cancer Monitor detected overall 79.35% of the tumors: 70.37% in low-grade and 92.11% in high-grade tumors. CONCLUSIONS The Xpert Bladder Cancer Monitor and Bladder EpiCheck test were found to perform very well in terms of sensitivity. Together, the 2 tests detected approximately 92.11% of high-grade tumors. Their specificity was high but could not reach the excellent value of cytology. The negative predictive value was the same for both tests and was higher than that for cytology, especially when the tests were used together (92.24%). These 2 new tests hold promise as urinary biomarkers. They may be used in combination to maximize sensitivity in a less invasive way, thereby reducing invasiveness in the follow-up of patients with non-muscle-invasive bladder cancer and decreasing discomfort for the patients as well as complications and costs.
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Affiliation(s)
- Emanuela Trenti
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy
| | - Stefan Pycha
- Faculty of Medicine, Riga Stradins University, Riga, Latvia
| | - Christine Mian
- Department of Pathology, Central Hospital of Bolzano, Bolzano, Italy
| | | | - Esther Hanspeter
- Department of Pathology, Central Hospital of Bolzano, Bolzano, Italy
| | - Mona Kafka
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | | | - Egils Vjaters
- Department of Urology, Riga Stradins University Hospital, Riga, Latvia
| | - Stephan Degener
- Department of Urology, Helios-Clinic Wuppertal, Witten Herdecke University, Wuppertal, Germany
| | - Armin Pycha
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy.,Medical School, Sigmund Freud Private University, Vienna, Austria
| | - Carolina D'Elia
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy
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13
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Trenti E, D'Elia C, Mian C, Schwienbacher C, Hanspeter E, Pycha A, Kafka M, Degener S, Danuser H, Roth S, Pycha A. Diagnostic predictive value of the Bladder EpiCheck test in the follow-up of patients with non-muscle-invasive bladder cancer. Cancer Cytopathol 2019; 127:465-469. [PMID: 31154670 DOI: 10.1002/cncy.22152] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2019] [Revised: 04/28/2019] [Accepted: 05/06/2019] [Indexed: 11/09/2022]
Abstract
BACKGROUND The objective of this study was to evaluate the diagnostic accuracy of the Bladder EpiCheck test in the follow-up of patients with non-muscle-invasive bladder cancer (NMIBC) and to compare it with the accuracy of urinary cytology, cystoscopy, and/or histology. METHODS In total, 243 patients were enrolled in the current study. Patients were evaluated by voided urine cytology, by the Bladder EpiCheck test, and by white-light cystoscopy. RESULTS Overall sensitivity was 33.3% for cytology, 62.3% for Bladder EpiCheck, and 66.7% for the 2 tests combined. The sensitivity of cytology increased from 7.7% in low-grade (LG) tumors to 66.6% in high-grade (HG) tumors; whereas, for the Bladder EpiCheck test, the sensitivity was 46.1% in LG tumors and 83.3% in HG tumors. Combined cytology and Bladder EpiCheck testing yielded an overall sensitivity of 56.4% for LG tumors and 90% for HG tumors. Overall specificity was 98.6% for cytology, 86.3% for Bladder EpiCheck, and 85.6% for the 2 tests combined. The positive predictive value was 92% for cytology and 68.2% for Bladder EpiCheck. For the 2 tests combined, it was 68.6%. The negative predictive value was similar for the 2 tests: 75.8% for cytology, 82.9% for Bladder EpiCheck, and 84.5% for the 2 tests combined. CONCLUSIONS The sensitivity of the Bladder EpiCheck test was significantly higher than that of cytology. The test performed very well in terms of specificity but could not reach the high value of cytology. The positive predictive value was higher for Bladder EpiCheck, whereas the negative predictive value was approximately the same for both tests.
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Affiliation(s)
- Emanuela Trenti
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy
| | - Carolina D'Elia
- Department of Pathology, Central Hospital of Bolzano, Bolzano, Italy
| | - Christine Mian
- Department of Pathology, Central Hospital of Bolzano, Bolzano, Italy
| | | | - Esther Hanspeter
- Department of Pathology, Central Hospital of Bolzano, Bolzano, Italy
| | - Alexander Pycha
- Department of Urology, Lucerne Canton Hospital, Lucerne, Switzerland
| | - Mona Kafka
- Department of Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - Stephan Degener
- Department of Urology, Helios-Klinikum Wuppertal, Witten Herdecke University, Wuppertal, Germany
| | - Hansjörg Danuser
- Department of Urology, Lucerne Canton Hospital, Lucerne, Switzerland
| | - Stephan Roth
- Department of Urology, Helios-Klinikum Wuppertal, Witten Herdecke University, Wuppertal, Germany
| | - Armin Pycha
- Department of Urology, Central Hospital of Bolzano, Bolzano, Italy.,Medical School, Sigmund Freud Private University, Vienna, Austria
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14
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Domingues FS, König E, Schwienbacher C, Volpato CB, Picard A, Cantaloni C, Mascalzoni D, Lackner P, Heimbach A, Hoffmann P, Stanzial F, Hicks AA, Parmeggiani L, Benedicenti F, Pellegrin S, Casara G, Pramstaller PP. Compound heterozygous SZT2 mutations in two siblings with early-onset epilepsy, intellectual disability and macrocephaly. Seizure 2019; 66:81-85. [PMID: 30818181 DOI: 10.1016/j.seizure.2018.12.021] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2018] [Revised: 12/02/2018] [Accepted: 12/22/2018] [Indexed: 01/22/2023] Open
Abstract
PURPOSE Mutations in SZT2 have been previously reported in several cases of early onset epilepsy and intellectual disability. In this study we investigate potential causal mutations in two male siblings affected by early onset epilepsy, intellectual disability and macrocephaly. METHODS We use family-based whole-exome sequencing to identify candidate variants. RESULTS We report the identification of two potential causal SZT2 mutations in compound heterozygous state. We observe considerable differences in the clinical phenotype severity of the two affected individuals. The cerebral MRI revealed no abnormalities in the older affected brother, while in the youngest one it revealed a right frontal polymicrogiria. Moreover, while good seizure control was achieved in the older affected individual the younger brother is affected by pharmacoresistant epilepsy, progressive spastic paraplegia, cortical myoclonus and a more severe intellectual disability. We also analyzed the relative location of the reported pathogenic mutations in the SZT2 protein. CONCLUSION Variable phenotypic expressivity is observed for this condition, while the location and type of mutations in SZT2 also has a potential impact on epilepsy severity. These findings extend our knowledge of epileptogenic conditions related to SZT2 and mTOR signaling.
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Affiliation(s)
- Francisco S Domingues
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.
| | - Eva König
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy; Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - Christine Schwienbacher
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Claudia B Volpato
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Anne Picard
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Chiara Cantaloni
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Deborah Mascalzoni
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Peter Lackner
- Department of Biosciences, University of Salzburg, Salzburg, Austria
| | - André Heimbach
- NGS Core Facility, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Per Hoffmann
- Human Genomics Research Group, Department of Biomedicine, University of Basel, Basel, Switzerland; Department of Genomics, Life & Brain Center, University of Bonn, Bonn, Germany
| | - Franco Stanzial
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Lucio Parmeggiani
- Child Neurology and Neurorehabilitation Unit, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Francesco Benedicenti
- Genetic Counseling Service, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Serena Pellegrin
- Child Neurology and Neurorehabilitation Unit, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Gianluca Casara
- Child Neurology and Neurorehabilitation Unit, Department of Pediatrics, Regional Hospital of Bolzano, Bolzano, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy; Department of Neurology, University of Lübeck, Lübeck, Germany
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15
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Soyal SM, Zara G, Ferger B, Felder TK, Kwik M, Nofziger C, Dossena S, Schwienbacher C, Hicks AA, Pramstaller PP, Paulmichl M, Weis S, Patsch W. The PPARGC1A locus and CNS-specific PGC-1α isoforms are associated with Parkinson's Disease. Neurobiol Dis 2019; 121:34-46. [DOI: 10.1016/j.nbd.2018.09.016] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2018] [Revised: 07/14/2018] [Accepted: 09/14/2018] [Indexed: 12/11/2022] Open
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16
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Zanon A, Kalvakuri S, Rakovic A, Foco L, Guida M, Schwienbacher C, Serafin A, Rudolph F, Trilck M, Grünewald A, Stanslowsky N, Wegner F, Giorgio V, Lavdas AA, Bodmer R, Pramstaller PP, Klein C, Hicks AA, Pichler I, Philip S. Corrigendum: SLP-2 interacts with Parkin in mitochondria and prevents mitochondrial dysfunction in Parkin-deficient human iPSC-derived neurons and Drosophila. Hum Mol Genet 2018; 28:1225. [PMID: 30517638 DOI: 10.1093/hmg/ddy408] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Affiliation(s)
- Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Sreehari Kalvakuri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | | | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Marianna Guida
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Christine Schwienbacher
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Alice Serafin
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | | | - Michaela Trilck
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany.,Molecular and Functional Neurobiology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, Belvaux, Luxembourg
| | | | - Florian Wegner
- Department of Neurology, Hannover Medical School, Hannover, Germany
| | | | - Alexandros A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, USA
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy.,Department of Neurology, General Central Hospital, Bolzano, Italy.,Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, Bolzano, Italy
| | - Seibler Philip
- Institute of Neurogenetics, University of Lübeck, Lübeck, Germany
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17
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D´Elia C, Pycha A, Folchini DM, Mian C, Hanspeter E, Schwienbacher C, Vjaters E, Pycha A, Trenti E. Diagnostic predictive value of Xpert Bladder Cancer Monitor in the follow-up of patients affected by non-muscle invasive bladder cancer. J Clin Pathol 2018; 72:140-144. [DOI: 10.1136/jclinpath-2018-205393] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2018] [Revised: 09/27/2018] [Accepted: 10/01/2018] [Indexed: 11/03/2022]
Abstract
AimsCystoscopy and urine cytology represent the gold standard for monitoring superficial bladder cancer (BC). Xpert BC Monitor is a new urinary marker based on the evaluation of five target mRNAs overexpressed in patients with bladder cancer. The aim of our study was to evaluate the diagnostic accuracy of Xpert BC Monitor in follow-up of patients with non-muscle invasive bladder cancer (NMIBC).Methods230 patients were included in this prospective study. Xpert BC Monitor cut-off was set to 0.5. Sensitivity, specificity, positive predictive value (PPV) and negative predictive value (NPV) of cytology, Xpert BC Monitor and their combination were calculated and compared with cystoscopy/histology.Results52/230 patients showed a NMIBC recurrence, 45 low grade (LG) and 7 high grade (HG). Overall sensitivity was 11.5% for cytology, 46.2% for Xpert BC Monitor and 48.1% for the two tests combined. Sensitivity of cytology increased from 4.4% in LG to 57.1% in HG tumours whereas for the Xpert BC Monitor it was 40% in LG and 85.7% in HG tumours. Combined cytology and Xpert BC Monitor yielded an overall sensitivity of 42% for LG and 85.7% for HG. Overall specificity was 97.2% for cytology, 77% for Xpert BC Monitor and 75.8% for the two tests.ConclusionsSensitivity for the Xpert BC Monitor Test was significantly higher than for cytology. The test performed very well in terms of specificity but could not reach the value of cytology, while PPV and NPV performed approximately the same for both tests.
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18
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Zanon A, Kalvakuri S, Rakovic A, Foco L, Guida M, Schwienbacher C, Serafin A, Rudolph F, Trilck M, Grünewald A, Stanslowsky N, Wegner F, Giorgio V, Lavdas AA, Bodmer R, Pramstaller PP, Klein C, Hicks AA, Pichler I, Seibler P. SLP-2 interacts with Parkin in mitochondria and prevents mitochondrial dysfunction in Parkin-deficient human iPSC-derived neurons and Drosophila. Hum Mol Genet 2017; 26:2412-2425. [PMID: 28379402 DOI: 10.1093/hmg/ddx132] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2016] [Accepted: 03/16/2017] [Indexed: 12/26/2022] Open
Abstract
Mutations in the Parkin gene (PARK2) have been linked to a recessive form of Parkinson's disease (PD) characterized by the loss of dopaminergic neurons in the substantia nigra. Deficiencies of mitochondrial respiratory chain complex I activity have been observed in the substantia nigra of PD patients, and loss of Parkin results in the reduction of complex I activity shown in various cell and animal models. Using co-immunoprecipitation and proximity ligation assays on endogenous proteins, we demonstrate that Parkin interacts with mitochondrial Stomatin-like protein 2 (SLP-2), which also binds the mitochondrial lipid cardiolipin and functions in the assembly of respiratory chain proteins. SH-SY5Y cells with a stable knockdown of Parkin or SLP-2, as well as induced pluripotent stem cell-derived neurons from Parkin mutation carriers, showed decreased complex I activity and altered mitochondrial network morphology. Importantly, induced expression of SLP-2 corrected for these mitochondrial alterations caused by reduced Parkin function in these cells. In-vivo Drosophila studies showed a genetic interaction of Parkin and SLP-2, and further, tissue-specific or global overexpression of SLP-2 transgenes rescued parkin mutant phenotypes, in particular loss of dopaminergic neurons, mitochondrial network structure, reduced ATP production, and flight and motor dysfunction. The physical and genetic interaction between Parkin and SLP-2 and the compensatory potential of SLP-2 suggest a functional epistatic relationship to Parkin and a protective role of SLP-2 in neurons. This finding places further emphasis on the significance of Parkin for the maintenance of mitochondrial function in neurons and provides a novel target for therapeutic strategies.
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Affiliation(s)
- Alessandra Zanon
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Sreehari Kalvakuri
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | | | - Luisa Foco
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Marianna Guida
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Christine Schwienbacher
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Alice Serafin
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Franziska Rudolph
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Michaela Trilck
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Anne Grünewald
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany.,Molecular and Functional Neurobiology Group, Luxembourg Centre for Systems Biomedicine, University of Luxembourg, L-4367 Belvaux, Luxembourg
| | - Nancy Stanslowsky
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany
| | - Florian Wegner
- Department of Neurology, Hannover Medical School, 30625 Hannover, Germany
| | | | - Alexandros A Lavdas
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Rolf Bodmer
- Development, Aging and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy.,Department of Neurology, General Central Hospital, 39100 Bolzano, Italy.,Department of Neurology, University of Lübeck, 23562 Lübeck, Germany
| | - Christine Klein
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
| | - Andrew A Hicks
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Irene Pichler
- Institute for Biomedicine, Eurac Research, Affiliated Institute of the University of Lübeck, 39100 Bolzano, Italy
| | - Philip Seibler
- Institute of Neurogenetics, University of Lübeck, 23562 Lübeck, Germany
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19
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Blankenburg H, Falla M, Schwienbacher C, Fabbrini G, Berardelli A, Pramstaller PP, Domingues FS. A Web Resource for Levodopa-Induced Dyskinesia Genetics in Parkinson's Disease. Neuroinformatics 2017; 15:297-300. [PMID: 28417316 DOI: 10.1007/s12021-017-9327-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Hagen Blankenburg
- Institute for Biomedicine, Eurac Research, Eurac Research, Bolzano, Italy.
| | - Marika Falla
- Institute for Biomedicine, Eurac Research, Eurac Research, Bolzano, Italy.,Department of Neurology, General Central Hospital, Bolzano, Italy.,Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy
| | | | - Giovanni Fabbrini
- Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy.,Neuromed Institute IRCCS, Pozzilli, Italy
| | - Alfredo Berardelli
- Department of Neurology and Psychiatry, Sapienza University of Rome, Rome, Italy.,Neuromed Institute IRCCS, Pozzilli, Italy
| | - Peter P Pramstaller
- Institute for Biomedicine, Eurac Research, Eurac Research, Bolzano, Italy.,Department of Neurology, General Central Hospital, Bolzano, Italy.,Department of Neurology, University of Lübeck, Lübeck, Germany
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20
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Noce D, Gögele M, Schwienbacher C, Caprioli G, De Grandi A, Foco L, Platzgummer S, Pramstaller PP, Pattaro C. Sequential recruitment of study participants may inflate genetic heritability estimates. Hum Genet 2017; 136:743-757. [PMID: 28374192 DOI: 10.1007/s00439-017-1785-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2016] [Accepted: 03/22/2017] [Indexed: 01/08/2023]
Abstract
After the success of genome-wide association studies to uncover complex trait loci, attempts to explain the remaining genetic heritability (h 2) are mainly focused on unraveling rare variant associations and gene-gene or gene-environment interactions. Little attention is paid to the possibility that h 2 estimates are inflated as a consequence of the epidemiological study design. We studied the time series of 54 biochemical traits in 4373 individuals from the Cooperative Health Research In South Tyrol (CHRIS) study, a pedigree-based study enrolling ten participants/day over several years, with close relatives preferentially invited within the same day. We observed distributional changes of measured traits over time. We hypothesized that the combination of such changes with the pedigree structure might generate a shared-environment component with consequent h 2 inflation. We performed variance components (VC) h 2 estimation for all traits after accounting for the enrollment period in a linear mixed model (two-stage approach). Accounting for the enrollment period caused a median h 2 reduction of 4%. For 9 traits, the reduction was of >20%. Results were confirmed by a Bayesian Markov chain Monte Carlo analysis with all VCs included at the same time (one-stage approach). The electrolytes were the traits most affected by the enrollment period. The h 2 inflation was independent of the h 2 magnitude, laboratory protocol changes, and length of the enrollment period. The enrollment process may induce shared-environment effects even under very stringent and standardized operating procedures, causing h 2 inflation. Including the day of participation as a random effect is a sensitive way to avoid overestimation.
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Affiliation(s)
- Damia Noce
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Affiliated to the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy.
| | - Martin Gögele
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Affiliated to the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
| | - Christine Schwienbacher
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Affiliated to the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
| | - Giulia Caprioli
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Affiliated to the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
| | - Alessandro De Grandi
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Affiliated to the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
| | - Luisa Foco
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Affiliated to the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
| | | | - Peter P Pramstaller
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Affiliated to the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy
- Department of Neurology, Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Cristian Pattaro
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Affiliated to the University of Lübeck, Via Galvani 31, 39100, Bolzano, Italy.
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21
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Pattaro C, Gögele M, Mascalzoni D, Melotti R, Schwienbacher C, De Grandi A, Foco L, D'Elia Y, Linder B, Fuchsberger C, Minelli C, Egger C, Kofink LS, Zanigni S, Schäfer T, Facheris MF, Smárason SV, Rossini A, Hicks AA, Weiss H, Pramstaller PP. The Cooperative Health Research in South Tyrol (CHRIS) study: rationale, objectives, and preliminary results. J Transl Med 2015; 13:348. [PMID: 26541195 PMCID: PMC4635524 DOI: 10.1186/s12967-015-0704-9] [Citation(s) in RCA: 57] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2015] [Accepted: 10/20/2015] [Indexed: 01/08/2023] Open
Abstract
The Cooperative Health Research In South Tyrol (CHRIS) study is a population-based study with a longitudinal lookout to investigate the genetic and molecular basis of age-related common chronic conditions and their interaction with life style and environment in the general population. All adults of the middle and upper Vinschgau/Val Venosta are invited, while 10,000 participants are anticipated by mid-2017. Family participation is encouraged for complete pedigree reconstruction and disease inheritance mapping. After a pilot study on the compliance with a paperless assessment mode, computer-assisted interviews have been implemented to screen for conditions of the cardiovascular, endocrine, metabolic, genitourinary, nervous, behavioral, and cognitive system. Fat intake, cardiac health, and tremor are assessed instrumentally. Nutrient intake, physical activity, and life-course smoking are measured semi-quantitatively. Participants are phenotyped for 73 blood and urine parameters and 60 aliquots per participant are biobanked (cryo-preserved urine, DNA, and whole and fractionated blood). Through liquid-chromatography mass-spectrometry analysis, metabolite profiling of the mitochondrial function is assessed. Samples are genotyped on 1 million variants with the Illumina HumanOmniExpressExome array and the first data release including 4570 fully phenotyped and genotyped samples is now available for analysis. Participants’ follow-up is foreseen 6 years after the first visit. The target population is characterized by long-term social stability and homogeneous environment which should both favor the identification of enriched genetic variants. The CHRIS cohort is a valuable resource to assess the contribution of genomics, metabolomics, and environmental factors to human health and disease. It is awaited that this will result in the identification of novel molecular targets for disease prevention and treatment.
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Affiliation(s)
- Cristian Pattaro
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy.
| | - Martin Gögele
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Deborah Mascalzoni
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Roberto Melotti
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Christine Schwienbacher
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Alessandro De Grandi
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Luisa Foco
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Yuri D'Elia
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Barbara Linder
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Christian Fuchsberger
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Cosetta Minelli
- Respiratory Epidemiology, Occupational Medicine and Public Health, National Heart and Lung Institute, Imperial College, London, UK
| | - Clemens Egger
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Lisa S Kofink
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Stefano Zanigni
- Functional MR Unit, Policlinico S. Orsola, Malpighi Bologna, Department of Biomedical and Neuromotor Sciences, University of Bologna, Bologna, Italy
| | - Torsten Schäfer
- Dermatological Practice, Kirchplatz 3, 87059, Immenstadt, Germany
| | | | - Sigurður V Smárason
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Alessandra Rossini
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Andrew A Hicks
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy
| | - Helmuth Weiss
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy.,Hospital of Schlanders/Silandro, Schlanders/Silandro, Italy
| | - Peter P Pramstaller
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC) (Affiliated to the University of Lübeck, Lübeck, Germany), Via Galvani 31, 39100, Bolzano/Bozen, Italy. .,Department of Neurology, Central Hospital, Bolzano, Italy. .,Department of Neurology, University of Lübeck, Lübeck, Germany.
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22
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Meraviglia V, Zanon A, Lavdas AA, Schwienbacher C, Silipigni R, Di Segni M, Chen HSV, Pramstaller PP, Hicks AA, Rossini A. Generation of Induced Pluripotent Stem Cells from Frozen Buffy Coats using Non-integrating Episomal Plasmids. J Vis Exp 2015:e52885. [PMID: 26131963 DOI: 10.3791/52885] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Somatic cells can be reprogrammed into induced pluripotent stem cells (iPSCs) by forcing the expression of four transcription factors (Oct-4, Sox-2, Klf-4, and c-Myc), typically expressed by human embryonic stem cells (hESCs). Due to their similarity with hESCs, iPSCs have become an important tool for potential patient-specific regenerative medicine, avoiding ethical issues associated with hESCs. In order to obtain cells suitable for clinical application, transgene-free iPSCs need to be generated to avoid transgene reactivation, altered gene expression and misguided differentiation. Moreover, a highly efficient and inexpensive reprogramming method is necessary to derive sufficient iPSCs for therapeutic purposes. Given this need, an efficient non-integrating episomal plasmid approach is the preferable choice for iPSC derivation. Currently the most common cell type used for reprogramming purposes are fibroblasts, the isolation of which requires tissue biopsy, an invasive surgical procedure for the patient. Therefore, human peripheral blood represents the most accessible and least invasive tissue for iPSC generation. In this study, a cost-effective and viral-free protocol using non-integrating episomal plasmids is reported for the generation of iPSCs from human peripheral blood mononuclear cells (PBMNCs) obtained from frozen buffy coats after whole blood centrifugation and without density gradient separation.
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Affiliation(s)
| | | | | | | | - Rosamaria Silipigni
- Laboratory of Medical Genetics, Fondazione IRCCS Ca´ Granda, Ospedale Maggiore Policlinico
| | - Marina Di Segni
- Laboratory of Medical Genetics, Fondazione IRCCS Ca´ Granda, Ospedale Maggiore Policlinico
| | - Huei-Sheng Vincent Chen
- Del E. Webb Center for Neuroscience, Aging & Stem Cell Research, Sanford-Burnham Medical Research Institute
| | | | - Andrew A Hicks
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC)
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23
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Benyamin B, Esko T, Ried JS, Radhakrishnan A, Vermeulen SH, Traglia M, Gögele M, Anderson D, Broer L, Podmore C, Luan J, Kutalik Z, Sanna S, van der Meer P, Tanaka T, Wang F, Westra HJ, Franke L, Mihailov E, Milani L, Hälldin J, Winkelmann J, Meitinger T, Thiery J, Peters A, Waldenberger M, Rendon A, Jolley J, Sambrook J, Kiemeney LA, Sweep FC, Sala CF, Schwienbacher C, Pichler I, Hui J, Demirkan A, Isaacs A, Amin N, Steri M, Waeber G, Verweij N, Powell JE, Nyholt DR, Heath AC, Madden PAF, Visscher PM, Wright MJ, Montgomery GW, Martin NG, Hernandez D, Bandinelli S, van der Harst P, Uda M, Vollenweider P, Scott RA, Langenberg C, Wareham NJ, van Duijn C, Beilby J, Pramstaller PP, Hicks AA, Ouwehand WH, Oexle K, Gieger C, Metspalu A, Camaschella C, Toniolo D, Swinkels DW, Whitfield JB. Corrigendum: Novel loci affecting iron homeostasis and their effects in individuals at risk for hemochromatosis. Nat Commun 2015; 6:6542. [PMID: 25817829 DOI: 10.1038/ncomms7542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022] Open
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24
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Serafin A, Foco L, Zanigni S, Blankenburg H, Picard A, Zanon A, Giannini G, Pichler I, Facheris MF, Cortelli P, Pramstaller PP, Hicks AA, Domingues FS, Schwienbacher C. Overexpression of blood microRNAs 103a, 30b, and 29a in L-dopa-treated patients with PD. Neurology 2015; 84:645-53. [PMID: 25596505 DOI: 10.1212/wnl.0000000000001258] [Citation(s) in RCA: 90] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
OBJECTIVE The aims of the present study were to profile the expression of several candidate microRNAs (miRNAs) in blood from L-dopa-treated and drug-naive patients with Parkinson disease (PD) vs unaffected controls and to interpret the miRNA expression data in a biological context. METHODS We analyzed RNAs from peripheral blood of 36 L-dopa-treated, 10 drug-naive patients with PD and unaffected controls matched 1:1 by sex and age. We evaluated expression by reverse transcription-quantitative real-time PCR, and we analyzed data using a 2-tailed paired t test. To detect miRNA targets, several miRNA resources were combined to generate an overall score for each candidate gene using weighted rank aggregation. RESULTS Significant overexpression of miR-103a-3p (p < 0.0001), miR-30b-5p (p = 0.002), and miR-29a-3p (p = 0.005) in treated patients with PD was observed, and promising candidate target genes for these were revealed by an integrated in silico analysis. CONCLUSIONS We revealed 3 candidate biomarkers for PD. miRNAs 30b-5p and 29a-3p replicated a documented deregulation in PD albeit opposite to published data, while for miR-103a-3p, we demonstrated for the first time an overexpression in treated patients with PD. Expression studies in patients and/or in isolated peripheral blood mononuclear cells before and after L-dopa administration are necessary to define the involvement of L-dopa treatment in the observed overexpression. Our in silico analysis to prioritize targets of deregulated miRNAs identified candidate target genes, including genes related to neurodegeneration and PD. Despite the preliminary character of our study, the results provide a rationale for further clarifying the role of the identified miRNAs in the pathogenesis of PD and for validating their diagnostic potential.
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Affiliation(s)
- Alice Serafin
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Luisa Foco
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Stefano Zanigni
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Hagen Blankenburg
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Anne Picard
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Alessandra Zanon
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Giulia Giannini
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Irene Pichler
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Maurizio F Facheris
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Pietro Cortelli
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Peter P Pramstaller
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Andrew A Hicks
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Francisco S Domingues
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany
| | - Christine Schwienbacher
- From the Center for Biomedicine (A.S., L.F., S.Z., H.B., A.P., A.Z., G.G., I.P., M.F.F., P.P.P., A.A.H., F.S.D., C.S.), European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Germany; Department of Neurology (S.Z., P.P.P.), General Central Hospital, Bolzano; IRCCS Institute of Neurological Sciences of Bologna (P.C.); Department of Biomedical and NeuroMotor Sciences (P.C.), Alma Mater Studiorum-University of Bologna, Italy; Department of Neurology (P.P.P.), University of Lübeck, Germany.
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25
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Serafin A, Foco L, Blankenburg H, Picard A, Zanigni S, Zanon A, Pramstaller PP, Hicks AA, Schwienbacher C. Identification of a set of endogenous reference genes for miRNA expression studies in Parkinson's disease blood samples. BMC Res Notes 2014; 7:715. [PMID: 25304816 PMCID: PMC4209045 DOI: 10.1186/1756-0500-7-715] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2014] [Accepted: 10/02/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Research on microRNAs (miRNAs) is becoming an increasingly attractive field, as these small RNA molecules are involved in several physiological functions and diseases. To date, only few studies have assessed the expression of blood miRNAs related to Parkinson's disease (PD) using microarray and quantitative real-time PCR (qRT-PCR). Measuring miRNA expression involves normalization of qRT-PCR data using endogenous reference genes for calibration, but their choice remains a delicate problem with serious impact on the resulting expression levels. The aim of the present study was to evaluate the suitability of a set of commonly used small RNAs as normalizers and to identify which of these miRNAs might be considered reliable reference genes in qRT-PCR expression analyses on PD blood samples. RESULTS Commonly used reference genes snoRNA RNU24, snRNA RNU6B, snoRNA Z30 and miR-103a-3p were selected from the literature. We then analyzed the effect of using these genes as reference, alone or in any possible combination, on the measured expression levels of the target genes miR-30b-5p and miR-29a-3p, which have been previously reported to be deregulated in PD blood samples. CONCLUSIONS We identified RNU24 and Z30 as a reliable and stable pair of reference genes in PD blood samples.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Christine Schwienbacher
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), 39100 Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany.
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26
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van Vliet-Ostaptchouk JV, Nuotio ML, Slagter SN, Doiron D, Fischer K, Foco L, Gaye A, Gögele M, Heier M, Hiekkalinna T, Joensuu A, Newby C, Pang C, Partinen E, Reischl E, Schwienbacher C, Tammesoo ML, Swertz MA, Burton P, Ferretti V, Fortier I, Giepmans L, Harris JR, Hillege HL, Holmen J, Jula A, Kootstra-Ros JE, Kvaløy K, Holmen TL, Männistö S, Metspalu A, Midthjell K, Murtagh MJ, Peters A, Pramstaller PP, Saaristo T, Salomaa V, Stolk RP, Uusitupa M, van der Harst P, van der Klauw MM, Waldenberger M, Perola M, Wolffenbuttel BHR. The prevalence of metabolic syndrome and metabolically healthy obesity in Europe: a collaborative analysis of ten large cohort studies. BMC Endocr Disord 2014; 14:9. [PMID: 24484869 PMCID: PMC3923238 DOI: 10.1186/1472-6823-14-9] [Citation(s) in RCA: 364] [Impact Index Per Article: 36.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/26/2014] [Accepted: 01/27/2014] [Indexed: 12/03/2022] Open
Abstract
BACKGROUND Not all obese subjects have an adverse metabolic profile predisposing them to developing type 2 diabetes or cardiovascular disease. The BioSHaRE-EU Healthy Obese Project aims to gain insights into the consequences of (healthy) obesity using data on risk factors and phenotypes across several large-scale cohort studies. Aim of this study was to describe the prevalence of obesity, metabolic syndrome (MetS) and metabolically healthy obesity (MHO) in ten participating studies. METHODS Ten different cohorts in seven countries were combined, using data transformed into a harmonized format. All participants were of European origin, with age 18-80 years. They had participated in a clinical examination for anthropometric and blood pressure measurements. Blood samples had been drawn for analysis of lipids and glucose. Presence of MetS was assessed in those with obesity (BMI ≥ 30 kg/m2) based on the 2001 NCEP ATP III criteria, as well as an adapted set of less strict criteria. MHO was defined as obesity, having none of the MetS components, and no previous diagnosis of cardiovascular disease. RESULTS Data for 163,517 individuals were available; 17% were obese (11,465 men and 16,612 women). The prevalence of obesity varied from 11.6% in the Italian CHRIS cohort to 26.3% in the German KORA cohort. The age-standardized percentage of obese subjects with MetS ranged in women from 24% in CHRIS to 65% in the Finnish Health2000 cohort, and in men from 43% in CHRIS to 78% in the Finnish DILGOM cohort, with elevated blood pressure the most frequently occurring factor contributing to the prevalence of the metabolic syndrome. The age-standardized prevalence of MHO varied in women from 7% in Health2000 to 28% in NCDS, and in men from 2% in DILGOM to 19% in CHRIS. MHO was more prevalent in women than in men, and decreased with age in both sexes. CONCLUSIONS Through a rigorous harmonization process, the BioSHaRE-EU consortium was able to compare key characteristics defining the metabolically healthy obese phenotype across ten cohort studies. There is considerable variability in the prevalence of healthy obesity across the different European populations studied, even when unified criteria were used to classify this phenotype.
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Affiliation(s)
- Jana V van Vliet-Ostaptchouk
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, HPC AA31, P.O. Box 30001, Groningen RB 9700, The Netherlands
| | - Marja-Liisa Nuotio
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Unit of Public Health Genomics, National Institute for Health and Welfare, Helsinki, Finland
| | - Sandra N Slagter
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, HPC AA31, P.O. Box 30001, Groningen RB 9700, The Netherlands
| | - Dany Doiron
- Research Institute of the McGill University of Health Centre, Montreal, Canada
| | - Krista Fischer
- University of Tartu, Estonian Genome Center, Tartu, Estonia
| | - Luisa Foco
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Bolzano, Italy
| | - Amadou Gaye
- Data to Knowledge Research Group, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Martin Gögele
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Bolzano, Italy
| | - Margit Heier
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Tero Hiekkalinna
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Unit of Public Health Genomics, National Institute for Health and Welfare, Helsinki, Finland
| | - Anni Joensuu
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Unit of Public Health Genomics, National Institute for Health and Welfare, Helsinki, Finland
| | - Christopher Newby
- Data to Knowledge Research Group, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Chao Pang
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Genomics Coordination Center, University of Groningen, Groningen Bioinformatics Center, and University Medical Center Groningen, Groningen, The Netherlands
| | - Eemil Partinen
- University of Tartu, Estonian Genome Center, Tartu, Estonia
| | - Eva Reischl
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | | | | | - Morris A Swertz
- Genomics Coordination Center, University of Groningen, Groningen Bioinformatics Center, and University Medical Center Groningen, Groningen, The Netherlands
| | - Paul Burton
- Data to Knowledge Research Group, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | | | - Isabel Fortier
- Research Institute of the McGill University of Health Centre, Montreal, Canada
| | - Lisette Giepmans
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jennifer R Harris
- Department of Genes and Environment, Division of Epidemiology, The Norwegian Institute of Public Health, Oslo, Norway
| | - Hans L Hillege
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Jostein Holmen
- HUNT Research Center, Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Antti Jula
- THL-National Institute for Health and Welfare, Helsinki, Finland
| | - Jenny E Kootstra-Ros
- Department of Laboratory Medicine, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Kirsti Kvaløy
- HUNT Research Center, Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Turid Lingaas Holmen
- HUNT Research Center, Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Satu Männistö
- Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland
| | | | - Kristian Midthjell
- HUNT Research Center, Department of Public Health and General Practice, Faculty of Medicine, Norwegian University of Science and Technology, Trondheim, Norway
| | - Madeleine J Murtagh
- Data to Knowledge Research Group, School of Social and Community Medicine, University of Bristol, Bristol, UK
| | - Annette Peters
- Institute of Epidemiology II, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Peter P Pramstaller
- Center for Biomedicine, European Academy of Bolzano/Bozen (EURAC), Bolzano, Italy
- Department of Neurology, Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
| | - Timo Saaristo
- Pirkanmaa hospital district and Finnish Diabetes Association, Tampere, Finland
| | - Veikko Salomaa
- THL-National Institute for Health and Welfare, Helsinki, Finland
| | - Ronald P Stolk
- Department of Epidemiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
- University of Groningen, University Medical Center Groningen, LifeLines Cohort Study, Groningen, The Netherlands
| | - Matti Uusitupa
- Institute of Public Health and Clinical Nutrition, University of Eastern Finland, and Research Unit, Kuopio University Hospital, Kuopio, Finland
| | - Pim van der Harst
- Department of Cardiology, University of Groningen, University Medical Center Groningen, Groningen, The Netherlands
| | - Melanie M van der Klauw
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, HPC AA31, P.O. Box 30001, Groningen RB 9700, The Netherlands
- University of Groningen, University Medical Center Groningen, LifeLines Cohort Study, Groningen, The Netherlands
| | - Melanie Waldenberger
- Research Unit of Molecular Epidemiology, Helmholtz Zentrum München, German Research Center for Environmental Health, Neuherberg, Germany
| | - Markus Perola
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Unit of Public Health Genomics, National Institute for Health and Welfare, Helsinki, Finland
- University of Tartu, Estonian Genome Center, Tartu, Estonia
| | - Bruce HR Wolffenbuttel
- Department of Endocrinology, University of Groningen, University Medical Center Groningen, HPC AA31, P.O. Box 30001, Groningen RB 9700, The Netherlands
- University of Groningen, University Medical Center Groningen, LifeLines Cohort Study, Groningen, The Netherlands
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27
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Schwienbacher C, Serafin A, Zanon A, Pramstaller PP, Pichler I, Hicks AA. Involvement of proprotein convertase PCSK7 in the regulation of systemic iron homeostasis. Hepatology 2013; 58:1860-1. [PMID: 23504908 DOI: 10.1002/hep.26392] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 03/04/2013] [Accepted: 03/05/2013] [Indexed: 12/07/2022]
Affiliation(s)
- Christine Schwienbacher
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, affiliated institute of the University of Lübeck, Lübeck, Germany
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28
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Minelli C, De Grandi A, Weichenberger CX, Gögele M, Modenese M, Attia J, Barrett JH, Boehnke M, Borsani G, Casari G, Fox CS, Freina T, Hicks AA, Marroni F, Parmigiani G, Pastore A, Pattaro C, Pfeufer A, Ruggeri F, Schwienbacher C, Taliun D, Pramstaller PP, Domingues FS, Thompson JR. Importance of different types of prior knowledge in selecting genome-wide findings for follow-up. Genet Epidemiol 2013; 37:205-13. [PMID: 23307621 DOI: 10.1002/gepi.21705] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/28/2012] [Accepted: 11/22/2012] [Indexed: 12/14/2022]
Abstract
Biological plausibility and other prior information could help select genome-wide association (GWA) findings for further follow-up, but there is no consensus on which types of knowledge should be considered or how to weight them. We used experts' opinions and empirical evidence to estimate the relative importance of 15 types of information at the single-nucleotide polymorphism (SNP) and gene levels. Opinions were elicited from 10 experts using a two-round Delphi survey. Empirical evidence was obtained by comparing the frequency of each type of characteristic in SNPs established as being associated with seven disease traits through GWA meta-analysis and independent replication, with the corresponding frequency in a randomly selected set of SNPs. SNP and gene characteristics were retrieved using a specially developed bioinformatics tool. Both the expert and the empirical evidence rated previous association in a meta-analysis or more than one study as conferring the highest relative probability of true association, whereas previous association in a single study ranked much lower. High relative probabilities were also observed for location in a functional protein domain, although location in a region evolutionarily conserved in vertebrates was ranked high by the data but not by the experts. Our empirical evidence did not support the importance attributed by the experts to whether the gene encodes a protein in a pathway or shows interactions relevant to the trait. Our findings provide insight into the selection and weighting of different types of knowledge in SNP or gene prioritization, and point to areas requiring further research.
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Affiliation(s)
- Cosetta Minelli
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy.
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29
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Thompson JR, Gögele M, Weichenberger CX, Modenese M, Attia J, Barrett JH, Boehnke M, De Grandi A, Domingues FS, Hicks AA, Marroni F, Pattaro C, Ruggeri F, Borsani G, Casari G, Parmigiani G, Pastore A, Pfeufer A, Schwienbacher C, Taliun D, Fox CS, Pramstaller PP, Minelli C. SNP prioritization using a Bayesian probability of association. Genet Epidemiol 2013; 37:214-21. [PMID: 23280596 PMCID: PMC3725584 DOI: 10.1002/gepi.21704] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2012] [Revised: 10/30/2012] [Accepted: 11/22/2012] [Indexed: 11/11/2022]
Abstract
Prioritization is the process whereby a set of possible candidate genes or SNPs is ranked so that the most promising can be taken forward into further studies. In a genome-wide association study, prioritization is usually based on the P-values alone, but researchers sometimes take account of external annotation information about the SNPs such as whether the SNP lies close to a good candidate gene. Using external information in this way is inherently subjective and is often not formalized, making the analysis difficult to reproduce. Building on previous work that has identified 14 important types of external information, we present an approximate Bayesian analysis that produces an estimate of the probability of association. The calculation combines four sources of information: the genome-wide data, SNP information derived from bioinformatics databases, empirical SNP weights, and the researchers' subjective prior opinions. The calculation is fast enough that it can be applied to millions of SNPS and although it does rely on subjective judgments, those judgments are made explicit so that the final SNP selection can be reproduced. We show that the resulting probability of association is intuitively more appealing than the P-value because it is easier to interpret and it makes allowance for the power of the study. We illustrate the use of the probability of association for SNP prioritization by applying it to a meta-analysis of kidney function genome-wide association studies and demonstrate that SNP selection performs better using the probability of association compared with P-values alone.
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Affiliation(s)
- John R Thompson
- Department of Health Sciences, University of Leicester, Leicester, United Kingdom.
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30
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Franceschini N, van Rooij F, Prins B, Feitosa M, Karakas M, Eckfeldt J, Folsom A, Kopp J, Vaez A, Andrews J, Baumert J, Boraska V, Broer L, Hayward C, Ngwa J, Okada Y, Polasek O, Westra HJ, Wang Y, Del Greco M. F, Glazer N, Kapur K, Kema I, Lopez L, Schillert A, Smith A, Winkler C, Zgaga L, Bandinelli S, Bergmann S, Boban M, Bochud M, Chen Y, Davies G, Dehghan A, Ding J, Doering A, Durda J, Ferrucci L, Franco O, Franke L, Gunjaca G, Hofman A, Hsu FC, Kolcic I, Kraja A, Kubo M, Lackner K, Launer L, Loehr L, Li G, Meisinger C, Nakamura Y, Schwienbacher C, Starr J, Takahashi A, Torlak V, Uitterlinden A, Vitart V, Waldenberger M, Wild P, Kirin M, Zeller T, Zemunik T, Zhang Q, Ziegler A, Blankenberg S, Boerwinkle E, Borecki I, Campbell H, Deary I, Frayling T, Gieger C, Harris T, Hicks A, Koenig W, O’Donnell C, Fox C, Pramstaller P, Psaty B, Reiner A, Rotter J, Rudan I, Snieder H, Tanaka T, van Duijn C, Vollenweider P, Waeber G, Wilson J, Witteman J, Wolffenbuttel B, Wright A, Wu Q, Liu Y, Jenny N, North K, Felix J, Alizadeh B, Cupples L, Perry J, Morris A, Morris AP. Discovery and fine mapping of serum protein loci through transethnic meta-analysis. Am J Hum Genet 2012; 91:744-53. [PMID: 23022100 DOI: 10.1016/j.ajhg.2012.08.021] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 06/18/2012] [Accepted: 08/23/2012] [Indexed: 10/27/2022] Open
Abstract
Many disorders are associated with altered serum protein concentrations, including malnutrition, cancer, and cardiovascular, kidney, and inflammatory diseases. Although these protein concentrations are highly heritable, relatively little is known about their underlying genetic determinants. Through transethnic meta-analysis of European-ancestry and Japanese genome-wide association studies, we identified six loci at genome-wide significance (p < 5 × 10(-8)) for serum albumin (HPN-SCN1B, GCKR-FNDC4, SERPINF2-WDR81, TNFRSF11A-ZCCHC2, FRMD5-WDR76, and RPS11-FCGRT, in up to 53,190 European-ancestry and 9,380 Japanese individuals) and three loci for total protein (TNFRS13B, 6q21.3, and ELL2, in up to 25,539 European-ancestry and 10,168 Japanese individuals). We observed little evidence of heterogeneity in allelic effects at these loci between groups of European and Japanese ancestry but obtained substantial improvements in the resolution of fine mapping of potential causal variants by leveraging transethnic differences in the distribution of linkage disequilibrium. We demonstrated a functional role for the most strongly associated serum albumin locus, HPN, for which Hpn knockout mice manifest low plasma albumin concentrations. Other loci associated with serum albumin harbor genes related to ribosome function, protein translation, and proteasomal degradation, whereas those associated with serum total protein include genes related to immune function. Our results highlight the advantages of transethnic meta-analysis for the discovery and fine mapping of complex trait loci and have provided initial insights into the underlying genetic architecture of serum protein concentrations and their association with human disease.
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Pichler I, Schwienbacher C, Zanon A, Fuchsberger C, Serafin A, Facheris MF, Marroni F, Pattaro C, Shen Y, Tellgren-Roth C, Gyllensten U, Gusella JF, Hicks AA, Pramstaller PP. Fine-mapping of restless legs locus 4 (RLS4) identifies a haplotype over the SPATS2L and KCTD18 genes. J Mol Neurosci 2012; 49:600-5. [PMID: 23054586 DOI: 10.1007/s12031-012-9891-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2012] [Accepted: 09/17/2012] [Indexed: 10/27/2022]
Abstract
Restless legs syndrome (RLS) is a sleep-related movement disorder that affects up to 15 % of the population. Linkage studies have identified several genomic loci in single families (12q, 14q, 9p, 2q, 20p and 16p, respectively). However, confirmation of these loci has not always been achieved, and causative mutations have not yet been identified. The locus on chromosome 2q33 (RLS4) was identified in two South Tyrolean families who shared a haplotype of microsatellite marker alleles across an 8.2-cM region. To pinpoint the gene localisation within RLS4, additional families from the same geographic region were evaluated, and linkage was replicated in one family. Within the candidate region, we initially found a haplotype of 23 single nucleotide polymorphism markers spanning 131.6 Kb shared by all affected members of the three linked families. Using a next generation sequencing approach, we further restricted the shared candidate region to 46.9 Kb over the potassium channel-related gene KCTD18 and exons 10-13 of SPATS2L.
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Affiliation(s)
- Irene Pichler
- Center for Biomedicine, European Academy Bozen/Bolzano (EURAC) (Affiliated institute of the University of Lübeck), Drususallee 1, 39100, Bozen/Bolzano, Italy
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32
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Tang W, Schwienbacher C, Lopez L, Ben-Shlomo Y, Oudot-Mellakh T, Johnson A, Samani N, Basu S, Gögele M, Davies G, Lowe G, Tregouet DA, Tan A, Pankow J, Tenesa A, Levy D, Volpato C, Rumley A, Gow A, Minelli C, Yarnell J, Porteous D, Starr J, Gallacher J, Boerwinkle E, Visscher P, Pramstaller P, Cushman M, Emilsson V, Plump A, Matijevic N, Morange PE, Deary I, Hicks A, Folsom A. Genetic associations for activated partial thromboplastin time and prothrombin time, their gene expression profiles, and risk of coronary artery disease. Am J Hum Genet 2012; 91:152-62. [PMID: 22703881 DOI: 10.1016/j.ajhg.2012.05.009] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2011] [Revised: 04/10/2012] [Accepted: 05/05/2012] [Indexed: 10/28/2022] Open
Abstract
Activated partial thromboplastin time (aPTT) and prothrombin time (PT) are clinical tests commonly used to screen for coagulation-factor deficiencies. One genome-wide association study (GWAS) has been reported previously for aPTT, but no GWAS has been reported for PT. We conducted a GWAS and meta-analysis to identify genetic loci for aPTT and PT. The GWAS for aPTT was conducted in 9,240 individuals of European ancestry from the Atherosclerosis Risk in Communities (ARIC) study, and the GWAS for PT was conducted in 2,583 participants from the Genetic Study of Three Population Microisolates in South Tyrol (MICROS) and the Lothian Birth Cohorts (LBC) of 1921 and 1936. Replication was assessed in 1,041 to 3,467 individuals. For aPTT, previously reported associations with KNG1, HRG, F11, F12, and ABO were confirmed. A second independent association in ABO was identified and replicated (rs8176704, p = 4.26 × 10(-24)). Pooling the ARIC and replication data yielded two additional loci in F5 (rs6028, p = 3.22 × 10(-9)) and AGBL1 (rs2469184, p = 3.61 × 10(-8)). For PT, significant associations were identified and confirmed in F7 (rs561241, p = 3.71 × 10(-56)) and PROCR/EDEM2 (rs2295888, p = 5.25 × 10(-13)). Assessment of existing gene expression and coronary artery disease (CAD) databases identified associations of five of the GWAS loci with altered gene expression and two with CAD. In summary, eight genetic loci that account for ∼29% of the variance in aPTT and two loci that account for ∼14% of the variance in PT were detected and supported by functional data.
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Pichler I, Minelli C, Sanna S, Tanaka T, Schwienbacher C, Naitza S, Porcu E, Pattaro C, Busonero F, Zanon A, Maschio A, Melville SA, Grazia Piras M, Longo DL, Guralnik J, Hernandez D, Bandinelli S, Aigner E, Murphy AT, Wroblewski V, Marroni F, Theurl I, Gnewuch C, Schadt E, Mitterer M, Schlessinger D, Ferrucci L, Witcher DR, Hicks AA, Weiss G, Uda M, Pramstaller PP. Identification of a common variant in the TFR2 gene implicated in the physiological regulation of serum iron levels. Hum Mol Genet 2010; 20:1232-40. [PMID: 21208937 DOI: 10.1093/hmg/ddq552] [Citation(s) in RCA: 58] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
The genetic determinants of variation in iron status are actively sought, but remain incompletely understood. Meta-analysis of two genome-wide association (GWA) studies and replication in three independent cohorts was performed to identify genetic loci associated in the general population with serum levels of iron and markers of iron status, including transferrin, ferritin, soluble transferrin receptor (sTfR) and sTfR-ferritin index. We identified and replicated a novel association of a common variant in the type-2 transferrin receptor (TFR2) gene with iron levels, with effect sizes highly consistent across samples. In addition, we identified and replicated an association between the HFE locus and ferritin and confirmed previously reported associations with the TF, TMPRSS6 and HFE genes. The five replicated variants were tested for association with expression levels of the corresponding genes in a publicly available data set of human liver samples, and nominally statistically significant expression differences by genotype were observed for all genes, although only rs3811647 in the TF gene survived the Bonferroni correction for multiple testing. In addition, we measured for the first time the effects of the common variant in TMPRSS6, rs4820268, on hepcidin mRNA in peripheral blood (n = 83 individuals) and on hepcidin levels in urine (n = 529) and observed an association in the same direction, though only borderline significant. These functional findings require confirmation in further studies with larger sample sizes, but they suggest that common variants in TMPRSS6 could modify the hepcidin-iron feedback loop in clinically unaffected individuals, thus making them more susceptible to imbalances of iron homeostasis.
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Affiliation(s)
- Irene Pichler
- Institute of Genetic Medicine, European Academy Bozen/Bolzano, 39100 Bolzano, Italy
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Oexle K, Ried JS, Hicks AA, Tanaka T, Hayward C, Bruegel M, Gögele M, Lichtner P, Müller-Myhsok B, Döring A, Illig T, Schwienbacher C, Minelli C, Pichler I, Fiedler GM, Thiery J, Rudan I, Wright AF, Campbell H, Ferrucci L, Bandinelli S, Pramstaller PP, Wichmann HE, Gieger C, Winkelmann J, Meitinger T. Novel association to the proprotein convertase PCSK7 gene locus revealed by analysing soluble transferrin receptor (sTfR) levels. Hum Mol Genet 2010; 20:1042-7. [PMID: 21149283 DOI: 10.1093/hmg/ddq538] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The level of body iron storage and the erythropoietic need for iron are indicated by the serum levels of ferritin and soluble transferrin receptor (sTfR), respectively. A meta-analysis of five genome-wide association studies on sTfR and ferritin revealed novel association to the PCSK7 and TMPRSS6 loci for sTfR and the HFE locus for both parameters. The PCSK7 association was the most significant (rs236918, P = 1.1 × 10E-27) suggesting that proprotein convertase 7, the gene product of PCSK7, may be involved in sTfR generation and/or iron homeostasis. Conditioning the sTfR analyses on transferrin saturation abolished the HFE signal and substantially diminished the TMPRSS6 signal while the PCSK7 association was unaffected, suggesting that the former may be mediated by transferrin saturation whereas the PCSK7-associated effect on sTfR generation appears to be more direct.
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Affiliation(s)
- Konrad Oexle
- Institute of Human Genetics, MRI, Technische Universität München, Munich, Germany.
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35
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Sotoodehnia N, Isaacs A, de Bakker PIW, Dörr M, Newton-Cheh C, Nolte IM, van der Harst P, Müller M, Eijgelsheim M, Alonso A, Hicks AA, Padmanabhan S, Hayward C, Smith AV, Polasek O, Giovannone S, Fu J, Magnani JW, Marciante KD, Pfeufer A, Gharib SA, Teumer A, Li M, Bis JC, Rivadeneira F, Aspelund T, Köttgen A, Johnson T, Rice K, Sie MPS, Wang YA, Klopp N, Fuchsberger C, Wild SH, Mateo Leach I, Estrada K, Völker U, Wright AF, Asselbergs FW, Qu J, Chakravarti A, Sinner MF, Kors JA, Petersmann A, Harris TB, Soliman EZ, Munroe PB, Psaty BM, Oostra BA, Cupples LA, Perz S, de Boer RA, Uitterlinden AG, Völzke H, Spector TD, Liu FY, Boerwinkle E, Dominiczak AF, Rotter JI, van Herpen G, Levy D, Wichmann HE, van Gilst WH, Witteman JCM, Kroemer HK, Kao WHL, Heckbert SR, Meitinger T, Hofman A, Campbell H, Folsom AR, van Veldhuisen DJ, Schwienbacher C, O'Donnell CJ, Volpato CB, Caulfield MJ, Connell JM, Launer L, Lu X, Franke L, Fehrmann RSN, te Meerman G, Groen HJM, Weersma RK, van den Berg LH, Wijmenga C, Ophoff RA, Navis G, Rudan I, Snieder H, Wilson JF, Pramstaller PP, Siscovick DS, Wang TJ, Gudnason V, van Duijn CM, Felix SB, Fishman GI, Jamshidi Y, Stricker BHC, Samani NJ, Kääb S, Arking DE. Common variants in 22 loci are associated with QRS duration and cardiac ventricular conduction. Nat Genet 2010; 42:1068-76. [PMID: 21076409 PMCID: PMC3338195 DOI: 10.1038/ng.716] [Citation(s) in RCA: 258] [Impact Index Per Article: 18.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2010] [Accepted: 10/19/2010] [Indexed: 12/16/2022]
Abstract
QRS interval on the electrocardiogram reflects ventricular depolarization and conduction time, and is a risk factor for mortality, sudden death, and heart failure. We performed a genome-wide association meta-analysis in 40,407 European-descent individuals from 14 studies, with further genotyping in 7170 additional Europeans, and identified 22 loci associated with QRS duration (P < 5 × 10−8). These loci map in or near genes in pathways with established roles in ventricular conduction such as sodium channels, transcription factors, and calcium-handling proteins, but also point to novel biologic processes, such as kinase inhibitors and genes related to tumorigenesis. We demonstrate that SCN10A, a gene at our most significant locus, is expressed in the mouse ventricular conduction system, and treatment with a selective SCN10A blocker prolongs QRS duration. These findings extend our current knowledge of ventricular depolarization and conduction.
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Affiliation(s)
- Nona Sotoodehnia
- Division of Cardiology, Department of Medicine, University of Washington, Seattle, Washington, USA.
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36
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Schwienbacher C, De Grandi A, Fuchsberger C, Facheris MF, Svaldi M, Wjst M, Pramstaller PP, Hicks AA. Copy number variation and association over T-cell receptor genes--influence of DNA source. Immunogenetics 2010; 62:561-7. [PMID: 20582410 DOI: 10.1007/s00251-010-0459-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2010] [Accepted: 06/04/2010] [Indexed: 11/30/2022]
Abstract
Genomic copy number variants (CNVs) are a common, heritable source of inter-individual differences in genomic sequence. Their influence on phenotypic variability and their involvement in the pathogenesis of several common diseases is well established and the object of many current studies. In the course of examining CNV association to various quantitative traits in a general population, we have detected a strong association of CNVs over the four TCR genes to lymphocyte and neutrophil numbers in blood. In a small replication series, we have further characterized the nature of these CNVs and found them not to be germline, but dependent on the origin of analysed DNA. Germline deletion and rearrangement around the T-cell receptor (TCR) genes naturally occurs in white blood cells. Blood DNA derived from persons with high lymphocyte counts generates variable intensity signals which behave like germline CNVs over these genes. As DNA containing a relative high proportion of these CNV-like events involving the TCR genes has the ability to influence genotype counts of SNPs in the regions of these genes, care should be taken in interpreting and replicating association signals on variants within these genes when blood-derived DNA is the only source of data.
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Hicks AA, Pramstaller PP, Johansson Å, Vitart V, Rudan I, Ugocsai P, Aulchenko Y, Franklin CS, Liebisch G, Erdmann J, Jonasson I, Zorkoltseva IV, Pattaro C, Hayward C, Isaacs A, Hengstenberg C, Campbell S, Gnewuch C, Janssens AC, Kirichenko AV, König IR, Marroni F, Polasek O, Demirkan A, Kolcic I, Schwienbacher C, Igl W, Biloglav Z, Witteman JCM, Pichler I, Zaboli G, Axenovich TI, Peters A, Schreiber S, Wichmann HE, Schunkert H, Hastie N, Oostra BA, Wild SH, Meitinger T, Gyllensten U, van Duijn CM, Wilson JF, Wright A, Schmitz G, Campbell H. Genetic determinants of circulating sphingolipid concentrations in European populations. PLoS Genet 2009; 5:e1000672. [PMID: 19798445 PMCID: PMC2745562 DOI: 10.1371/journal.pgen.1000672] [Citation(s) in RCA: 155] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2009] [Accepted: 09/02/2009] [Indexed: 01/01/2023] Open
Abstract
Sphingolipids have essential roles as structural components of cell membranes and in cell signalling, and disruption of their metabolism causes several diseases, with diverse neurological, psychiatric, and metabolic consequences. Increasingly, variants within a few of the genes that encode enzymes involved in sphingolipid metabolism are being associated with complex disease phenotypes. Direct experimental evidence supports a role of specific sphingolipid species in several common complex chronic disease processes including atherosclerotic plaque formation, myocardial infarction (MI), cardiomyopathy, pancreatic beta-cell failure, insulin resistance, and type 2 diabetes mellitus. Therefore, sphingolipids represent novel and important intermediate phenotypes for genetic analysis, yet little is known about the major genetic variants that influence their circulating levels in the general population. We performed a genome-wide association study (GWAS) between 318,237 single-nucleotide polymorphisms (SNPs) and levels of circulating sphingomyelin (SM), dihydrosphingomyelin (Dih-SM), ceramide (Cer), and glucosylceramide (GluCer) single lipid species (33 traits); and 43 matched metabolite ratios measured in 4,400 subjects from five diverse European populations. Associated variants (32) in five genomic regions were identified with genome-wide significant corrected p-values ranging down to 9.08x10(-66). The strongest associations were observed in or near 7 genes functionally involved in ceramide biosynthesis and trafficking: SPTLC3, LASS4, SGPP1, ATP10D, and FADS1-3. Variants in 3 loci (ATP10D, FADS3, and SPTLC3) associate with MI in a series of three German MI studies. An additional 70 variants across 23 candidate genes involved in sphingolipid-metabolizing pathways also demonstrate association (p = 10(-4) or less). Circulating concentrations of several key components in sphingolipid metabolism are thus under strong genetic control, and variants in these loci can be tested for a role in the development of common cardiovascular, metabolic, neurological, and psychiatric diseases.
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Affiliation(s)
- Andrew A. Hicks
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Peter P. Pramstaller
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Department of Neurology, General Central Hospital, Bolzano, Italy
- Department of Neurology, University of Lübeck, Lübeck, Germany
- * E-mail: (PPP); (HC)
| | - Åsa Johansson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Veronique Vitart
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Igor Rudan
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
- Croatian Centre for Global Health, Faculty of Medicine, University of Split, Split, Croatia
- Gen-info Ltd, Zagreb, Croatia
| | - Peter Ugocsai
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Yurii Aulchenko
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Gerhard Liebisch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | | | - Inger Jonasson
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Cristian Pattaro
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Caroline Hayward
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Aaron Isaacs
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Christian Hengstenberg
- Klinik und Poliklinik für Innere Medizin II, Universität Regensburg, Regensburg, Germany
| | - Susan Campbell
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Carsten Gnewuch
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - A. CecileJ.W. Janssens
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | | | - Inke R. König
- Institut für Medizinische Biometrie und Statistik, University of Lübeck, Lübeck, Germany
| | - Fabio Marroni
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Ozren Polasek
- Gen-info Ltd, Zagreb, Croatia
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | - Ayse Demirkan
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Ivana Kolcic
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | - Christine Schwienbacher
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Ferrara, Italy
| | - Wilmar Igl
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Zrinka Biloglav
- Andrija Stampar School of Public Health, Faculty of Medicine, University of Zagreb, Zagreb, Croatia
| | | | - Irene Pichler
- Institute of Genetic Medicine, European Academy Bozen/Bolzano (EURAC), Bolzano, Italy, Affiliated Institute of the University of Lübeck, Lübeck, Germany
| | - Ghazal Zaboli
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | | | - Annette Peters
- Institute of Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
| | - Stefan Schreiber
- Institut für Klinische Molekularbiologie, Christian-Albrechts Universität, Kiel, Germany
| | - H.-Erich Wichmann
- Institute of Epidemiology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany
- Institute of Medical Information Science, Biometry and Epidemiology, Chair of Epidemiology, LMU Munich, Germany
| | | | - Nick Hastie
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Ben A. Oostra
- Department of Clinical Genetics, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Sarah H. Wild
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Ulf Gyllensten
- Department of Genetics and Pathology, Rudbeck Laboratory, Uppsala University, Uppsala, Sweden
| | - Cornelia M. van Duijn
- Department of Epidemiology, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - James F. Wilson
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Alan Wright
- MRC Human Genetics Unit, IGMM, Western General Hospital, Edinburgh, United Kingdom
| | - Gerd Schmitz
- Institute for Clinical Chemistry and Laboratory Medicine, University Hospital Regensburg, Regensburg, Germany
| | - Harry Campbell
- Centre for Population Health Sciences, University of Edinburgh, Edinburgh, United Kingdom
- * E-mail: (PPP); (HC)
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38
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Sparago A, Russo S, Cerrato F, Ferraiuolo S, Castorina P, Selicorni A, Schwienbacher C, Negrini M, Ferrero GB, Silengo MC, Anichini C, Larizza L, Riccio A. Mechanisms causing imprinting defects in familial Beckwith-Wiedemann syndrome with Wilms' tumour. Hum Mol Genet 2006; 16:254-64. [PMID: 17158821 DOI: 10.1093/hmg/ddl448] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The imprinted expression of the IGF2 and H19 genes is controlled by the Imprinting Centre 1 (IC1) at chromosome 11p15.5. This is a methylation-sensitive chromatin insulator that works by binding the zinc-finger protein CTCF in a parent-specific manner. Microdeletions abolishing some of the CTCF target sites (CTSs) of IC1 have been associated with the Beckwith-Wiedemann syndrome (BWS). However, the link between these mutations and the molecular and clinical phenotypes was debated. We have identified two novel families with IC1 deletions, in which individuals with the clinical features of the BWS are present in multiple generations. By analysing the methylation pattern at the IGF2-H19 locus together with the clinical phenotypes in the individuals with maternal and those with paternal transmission of five different deletions, we demonstrate that maternal transmission of 1.4-1.8 kb deletions in the IC1 region co-segregates with the hypermethylation of the residual CTSs and BWS phenotype with complete penetrance, whereas normal phenotype is observed upon paternal transmission. Although gene expression could not be assayed in all cases, the methylation detected at the IGF2 DMR2 and H19 promoter suggests that IC1 hypermethylation is consistently associated with biallelic activation of IGF2 and biallelic silencing of H19. Comparison of these deletions with a 2.2 kb one previously reported by another group indicates that the spacing of the CTSs on the deleted allele is critical for the gain of the abnormal methylation and penetrance of the clinical phenotype. Furthermore, we observe that the hypermethylation resulting from the deletions is always mosaic, suggesting that the epigenetic defect at the IGF2-H19 locus is established post-zygotically and may cause body asymmetry and heterogeneity of the clinical phenotype. Finally, the IC1 microdeletions are associated with a high incidence of Wilms' tumour, making their molecular diagnosis particularly important for genetic counselling and tumour surveillance at follow-up.
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Affiliation(s)
- Angela Sparago
- Dipartimento di Scienze Ambientali, Seconda Università di Napoli, via Vivaldi 43, 81100 Caserta, Italy
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39
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Rosati R, La Starza R, Veronese A, Aventin A, Schwienbacher C, Vallespi T, Negrini M, Martelli MF, Mecucci C. NUP98 is fused to the NSD3 gene in acute myeloid leukemia associated with t(8;11)(p11.2;p15). Blood 2002; 99:3857-60. [PMID: 11986249 DOI: 10.1182/blood.v99.10.3857] [Citation(s) in RCA: 136] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Fusion between the NUP98 and NSD3 genes in a patient with acute myeloid leukemia associated with t(8;11)(p11.2;p15), is reported for the first time. The t(8;11)(p11.2;p15) was identified by classical cytogenetics. Fluorescence in situ hybridization (FISH) analysis revealed a split signal with a mix of BAC 118H17 and 290A12, indicating the translocation disrupted NUP98. FISH restriction at 8p11-12 showed a split of BAC 350N15. Molecular investigations into candidate genes in this BAC showed the NUP98 fusion partner at 8p11.2 was the NSD3 gene. To date the NSD3 gene has never been implicated in hematologic malignancies.
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Affiliation(s)
- Roberto Rosati
- Hematology and Bone Marrow Transplantation Unit, University of Perugia, Italy
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40
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Scelfo RAM, Schwienbacher C, Veronese A, Gramantieri L, Bolondi L, Querzoli P, Nenci I, Calin GA, Angioni A, Barbanti-Brodano G, Negrini M. Loss of methylation at chromosome 11p15.5 is common in human adult tumors. Oncogene 2002; 21:2564-72. [PMID: 11971191 DOI: 10.1038/sj.onc.1205336] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2001] [Revised: 01/10/2002] [Accepted: 01/11/2002] [Indexed: 11/09/2022]
Abstract
Chromosome 11p15 deletion is frequent in human tumors, suggesting the presence of at least one tumor suppressor gene within this region. While mutation analyses of local genes revealed only rare mutations, we have previously described a mechanism, gain of imprinting, that leads to loss of expression of genes located on the maternal 11p15 chromosome in human hepatocarcinomas. Loss of expression was often associated with loss of maternal-specific methylation at the KvDMR1 locus. Here, we show that loss of the maternal KvDMR1 methylation is common, ranging from 30 to 50%, to a variety of adult neoplasms, including liver, breast, cervical and gastric carcinomas. We found that other 11p15.5 loci were concomitantly hypomethylated, indicating that loss of KvDMR1 methylation occurred in the context of a common mechanism affecting the methylation of a large 11p15 subchromosomal domain. These epigenetic abnormalities were not detected in any normal somatic tissue. Therefore, it seems possible that, contrary to the repression of promoter activity caused by hypermethylation, loss of gene expression at 11p15.5 may result from the activation, by hypomethylation, of one or more negative regulatory elements.
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Affiliation(s)
- Rosaria A M Scelfo
- Dipartimento di Medicina Sperimentale e Diagnostica, Università di Ferrara, Via Luigi Borsari 46, 44100 Ferrara, Italy
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41
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Schwienbacher C, Gramantieri L, Scelfo R, Veronese A, Calin GA, Bolondi L, Croce CM, Barbanti-Brodano G, Negrini M. Gain of imprinting at chromosome 11p15: A pathogenetic mechanism identified in human hepatocarcinomas. Proc Natl Acad Sci U S A 2000; 97:5445-9. [PMID: 10779553 PMCID: PMC25848 DOI: 10.1073/pnas.090087497] [Citation(s) in RCA: 66] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Genomic imprinting is a reversible condition that causes parental-specific silencing of maternally or paternally inherited genes. Analysis of DNA and RNA from 52 human hepatocarcinoma samples revealed abnormal imprinting of genes located at chromosome 11p15 in 51% of 37 informative samples. The most frequently detected abnormality was gain of imprinting, which led to loss of expression of genes present on the maternal chromosome. As compared with matched normal liver tissue, hepatocellular carcinomas showed extinction or significant reduction of expression of one of the alleles of the CDKN1C, SLC22A1L, and IGF2 genes. Loss of maternal-specific methylation at the KvDMR1 locus in hepatocarcinoma correlated with abnormal expression of CDKN1C and IGF2, suggesting a function for KvDMR1 as a long-range imprinting center active in adult tissues. These results point to the role of epigenetic mechanisms leading to loss of expression of imprinted genes at chromosome region 11p15 in human tumors.
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Affiliation(s)
- C Schwienbacher
- Dipartimento di Medicina Sperimentale e Diagnostica, Università di Ferrara, via Luigi Borsari 46, 44100 Ferrara, Italy
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42
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Schwienbacher C, Angioni A, Scelfo R, Veronese A, Calin GA, Massazza G, Hatada I, Barbanti-Brodano G, Negrini M. Abnormal RNA expression of 11p15 imprinted genes and kidney developmental genes in Wilms' tumor. Cancer Res 2000; 60:1521-5. [PMID: 10749116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/16/2023]
Abstract
Wilms' tumor (WT) is caused by abnormal development of embryonal kidney cells. WT cells are frequently affected by deletions or functional inactivation of maternal alleles at chromosome 11p15, which indicates that the loss of maternally expressed genes in this region plays an important role in WT pathogenesis. Maternally expressed genes indeed exist within an imprinted region at 11p15.5. Among these, BWR1C is highly expressed in fetal but not in adult kidney, which suggests that it may fulfil an important role in kidney development. Here, we demonstrate that the lack of BWR1C expression is common in WT. Its homology with the proapoptotic gene TDAG51 suggests that the loss of BWR1C expression may be relevant in WT development. In addition, the analysis of the expression of other 11p15 imprinted genes and kidney-developmentally regulated genes indicates that IGF2 overexpression, inappropriate coexpression of RET and GDNF and, in some cases, down-regulation of CDKN1C may also play an important role in the pathogenesis of WT. Our results add new elements to the understanding of the biological basis of WT, which may have implications for WT diagnosis and therapy.
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Affiliation(s)
- C Schwienbacher
- Department of Experimental and Diagnostic Medicine, Interdepartment Center for Biotechnology, University of Ferrara, Italy
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43
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Rüdiger M, Korneeva N, Schwienbacher C, Weiss EE, Jockusch BM. Differential actin organization by vinculin isoforms: implications for cell type-specific microfilament anchorage. FEBS Lett 1998; 431:49-54. [PMID: 9684863 DOI: 10.1016/s0014-5793(98)00723-6] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Vinculin is found in all adherens junctions, while metavinculin, a larger splice variant, is coexpressed with vinculin only in smooth and cardiac muscle. To understand the significance of metavinculin expression, we compared ligand binding between turkey vinculin and metavinculin. Residues 1-258 were found essential for head-tail interactions in both proteins. The tail domains (VT and MVT, respectively) both bind to F-actin. However, while VT bundles F-actin, MVT generates highly viscous F-actin webs. In transfected PtK2 cells, VT causes F-actin needles or coils, while MVT-expressing cells display a diffuse F-actin distribution. Thus, the MVT-specific insert induces an F-actin supraorganization different from the VT-based form, suggesting that metavinculin has a specific role in muscle.
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Affiliation(s)
- M Rüdiger
- Cell Biology, Zoological Institute, Technical University Braunschweig, Germany
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44
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Schwienbacher C, Sabbioni S, Campi M, Veronese A, Bernardi G, Menegatti A, Hatada I, Mukai T, Ohashi H, Barbanti-Brodano G, Croce CM, Negrini M. Transcriptional map of 170-kb region at chromosome 11p15.5: identification and mutational analysis of the BWR1A gene reveals the presence of mutations in tumor samples. Proc Natl Acad Sci U S A 1998; 95:3873-8. [PMID: 9520460 PMCID: PMC19930 DOI: 10.1073/pnas.95.7.3873] [Citation(s) in RCA: 42] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Chromosome region 11p15.5 harbors unidentified genes involved in neoplasms and in the genetic disease Beckwith-Wiedemann syndrome. The genetic analysis of a 170-kb region at 11p15.5 between loci D11S601 and D11S679 resulted in the identification of six transcriptional units. Three genes, hNAP2, CDKN1C, and KVLQT1, are well characterized, whereas three genes are novel. The three additional genes were designated BWR1A, BWR1B, and BWR1C. Full-length cDNAs for these three genes were cloned and nucleotide sequences were determined. While our work was in progress, BWR1C cDNA was described as IPL [Qian, N., Franck, D., O'Keefe, D., Dao, D. , Zhao, L., Yuan, L., Wang, Q., Keating, M., Walsh, C. & Tycko, B. (1997) Hum. Mol. Genet. 6, 2021-2029]. The cloning and mapping of these genes together with the fine mapping of the three known genes indicates that the transcriptional map of this region is likely to be complete. Because this region frequently is altered in neoplasms and in the genetic disease Beckwith-Wiedemann syndrome, we carried out a mutational analysis in tumor cell lines and Beckwith-Wiedemann syndrome samples that resulted in the identification of genetic alterations in the BWR1A gene: an insertion that introduced a stop codon in the breast cancer cell line BT549 and a point mutation in the rhabdomyosarcoma cell line TE125-T. These results indicate that BWR1A may play a role in tumorigenesis.
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Affiliation(s)
- C Schwienbacher
- Department of Experimental and Diagnostic Medicine, Section of Microbiology, and Interdepartment Center for Biotechnology, University of Ferrara, 44100, Ferrara, Italy
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45
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Schwienbacher C, Sabbioni S, Barbanti-Brodano G, Negrini M. Refined subchromosomal location of 21 expressed sequence tags from unknown genes at region 11p15. Eur J Hum Genet 1997; 5:214-7. [PMID: 9359042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
Twenty-one expressed sequence tags (ESTs) belonging to unidentified transcripts were mapped to 9 intervals at 11p 15.5-p15.3. Thirteen were mapped to a region of an estimated size of 7 Mb with the help of a YAC contig. The remaining eight were mapped outside this region, and the centromeric or telomeric position of the ESTs relative to the YAC contig was defined with the help of a cellular hybrid containing a derivative chromosome 11 with a break-point within the region covered by the contig. The average size of the intervals, where the ESTs were mapped, was estimated to be 0.3-0.4 Mb. The refinement of the chromosomal location of these ESTs could be of great help in the identification of potential candidate genes for disease locus mapping at 11p15.
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Affiliation(s)
- C Schwienbacher
- Department of Experimental and Diagnostic Medicine, University of Ferrara, Italy
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46
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Schwienbacher C, Sabbioni S, Barbanti-Brodano G, Negrini M. Refined Subchromosomal Location of 21 Expressed Sequence Tags from Unknown Genes at Region 11p15. Eur J Hum Genet 1997. [DOI: 10.1159/000484766] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
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47
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Grazi E, Magri E, Schwienbacher C, Trombetta G. A model relating protein osmotic pressure to the stiffness of the cross-bridge components and the contractile force of skeletal muscle. Eur J Biochem 1996; 241:25-31. [PMID: 8898884 DOI: 10.1111/j.1432-1033.1996.0025t.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We have modeled the effect of protein osmotic pressure on the orientation of the monomer in F-actin, in tropomyosin-F-actin, in the myosin subfragment-1 decorated F-actin and in the myosin subfragment-1 decorated tropomyosin-F-actin. According to the model, at the physiological protein osmotic pressure (18 kPa), the elastic moduli by bending of the monomer in F-actin and in tropomyosin-F-actin are calculated to be 4.74 MPa and 5.8 MPa, respectively. The elastic moduli by bending of the monomer in the myosin subfragment-1 decorated F-actin and in the myosin subfragment-1 decorated tropomyosin-F-actin are calculated to be 22MPa and 22.3MPa, respectively. These latter values are in excellent agreement with the values of the elastic moduli by stretching found for the fibres of frog and rabbit muscle. We have also calculated that, at the physiological protein osmotic pressure, the myosin subfragment-1 decorated F-actin rigor complex can develop a force of 3.96 pN, a force correctly oriented to promote the sliding of the actin filament toward the center of the sarcomere. The magnitude of this force is comparable to that reported for intact skeletal muscle. In contrast, the myosin subfragment-1 decorated tropomyosin-F-actin rigor complex develops a much smaller driving force, that favours relaxation. Apparently tropomyosin uncouples the osmotic and the mechanical event. It is proposed that the elastic energy for muscle contraction is provided by protein osmotic pressure.
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Affiliation(s)
- E Grazi
- Dipartimento di Biochimica e Biología Molecolare, Università di Ferrara, Italy
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48
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Grazi E, Magri E, Schwienbacher C, Trombetta G. The stiffness of the crossbridge is a function of the intrinsic protein osmotic pressure generated by the crossbridge itself. FEBS Lett 1996. [DOI: 10.1016/0014-5793(96)81382-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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49
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Grazi E, Magri E, Schwienbacher C, Trombetta G. The stiffness of the crossbridge is a function of the intrinsic protein osmotic pressure generated by the crossbridge itself. FEBS Lett 1996; 387:101-4. [PMID: 8674527 DOI: 10.1016/0014-5793(96)00481-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
A model is presented that makes it possible to determine the stiffness of the crossbridge from protein osmotic stress experiments. The model was elaborated while studying the osmotic properties of F-actin and of myosin subfragment-1 F-actin. These studies showed that the elastic modulus by bending of the monomer is directly related to the intrinsic protein osmotic pressure of the system. At a protein osmotic pressure of 1.8 x 10(5) dynes/cm2, the physiological protein osmotic pressure of frog skeletal muscle, it was found that the elastic moduli by bending of the monomer in F-actin and in the myosin subfragment-1 decorated F-actin are 6.5 X 10(7) and 3.3 X 10(8) dynes/cm2, respectively. The value of the elastic modulus by bending of the monomer in the myosin subfragment-1 decorated F-actin compares favorably with the values of the elastic modulus by stretching determined in skeletal muscle fibres.
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Affiliation(s)
- E Grazi
- Dipartimento di Biochimica e Biologia Molecolare, Università di Ferrara, Italy
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50
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Abstract
Using protein kinase C, we have studied the influence of intramolecular interactions on phosphorylation in vinculin. We show that vinculin and its 90 kDa head and 29/27 kDa tail fragments, generated by V8 proteolytic cleavage, are differentially phosphorylated. While intact vinculin and the isolated head domain are only weakly labelled, the isolated tail fragment is much more strongly phosphorylated. In the presence of the tail, the head is fully protected from the kinase. These data are consistent with our observation that native vinculin is primarily phosphorylated within the tail domain and suggest a function of vinculin phosphorylation in the regulation of the vinculin conformation.
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Affiliation(s)
- C Schwienbacher
- Cell Biology-Zoological Institute, Technical University Braunschweig, Germany
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