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Lesch C, Uhr K, Vollmer M, Raschidi R, Nessel R, Kallinowski F. Standardized suturing can prevent slackening or bursting suture lines in midline abdominal incisions and defects. Hernia 2022; 26:1611-1623. [PMID: 35997898 PMCID: PMC9684257 DOI: 10.1007/s10029-022-02659-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [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: 05/26/2022] [Accepted: 07/20/2022] [Indexed: 12/02/2022]
Abstract
Purpose Incisional hernias often follow open abdominal surgery. A small-stitch–small-bite suture might close the incision durably. We analyzed specific details of this closure technique and assessed their influence on the closure stability. Methods The effects of cyclic loads, simulating coughs were investigated on a bench test. We prepared porcine bellies in the median line and bovine flanks parallel to the muscle fibers with 15 cm long incisions. Then we punched round or rhomboid defects with a diameter of 5–10 cm into the center of the incision. Monomax® 2–0 and Maxon® 1 and 2–0 were used as suture materials. We tested the durability of the closure with pressure impacts of 210 mmHg repeated 425 times. Throughout the experiments, we modified the suturing technique, the surgeon, the tissue tension, the defect size and shape and the suture diameter. Results Standardizing the suture technique improved the durability of the closure significantly. Any other variations showed minor influences after standardization. All incisions with round defects up to 7.5 cm width withstood 425 impacts using standardized suturing. Unstandardized sutures failed in all cases. When closing an incision with a 10 cm wide defect, the tissues ruptured frequently next to the suture line. We defined criteria to standardize this suturing technique. For the first time, we developed a suture factor related to the durability of a sutured tissue closure. We integrated the suture factor into the concept of biomechanically durable repairs. Conclusions Suturing the abdominal wall with a standardized suturing technique improves its durability significantly.
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Affiliation(s)
- C Lesch
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany.
| | - K Uhr
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
| | - M Vollmer
- Hamburg University of Technology, Biomechanics, Denickestrasse 15, 21073, Hamburg, Germany
| | - R Raschidi
- Department Allgemein- Und Viszeralchirurgie, Spital Walenstadt, St. Gallen, Switzerland
| | - R Nessel
- General, Visceral and Pediatric Surgery, Klinikum Am Gesundbrunnen, Am Gesundbrunnen 20-26, 74078, Heilbronn, Germany
| | - F Kallinowski
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Im Neuenheimer Feld 410, 69120, Heidelberg, Germany
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2
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Kallinowski F, Ludwig Y, Gutjahr D, Gerhard C, Schulte-Hörmann H, Krimmel L, Lesch C, Uhr K, Lösel P, Voss S, Heuveline V, Vollmer M, Görich J, Nessel R. P024 BIOMECHANICAL INFLUENCES TO BE CONSIDERED FOR A DURABLE INCISIONAL HERNIA REPAIR. Br J Surg 2021. [DOI: 10.1093/bjs/znab395.023] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Abstract
Aim
Recurrence indicates a failed repair. Which biomechanical factors have to be considered to reduce failure rates? How can surgeons enhance the interface between mesh and tissue?
Material and Methods
The strength of the mesh-tissue interface was evaluated by cyclic loading. A self-made bench test was used to apply dynamic intermittent strain (DIS) to model preparations in order to evaluate the tissue quality and the material properties of hernia meshes and fixation devices.
The influences and the properties were condensed in coefficients representing their relative strengths. The strain of the individual human abdominal wall were determined with computerized tomography at rest and during Valsalva’s maneuver.
Results
The strain observed in porcine, bovine and human tissue was in the same range. Tissue samples exhibited both brittle and ductile failure patterns. Both the load duration and the peak load increased destruction. Stress concentration elevated failure rates. Regional areas of distorsions increase stress concentrations. Hernia repair has to counteract individual strain levels. Measures to improve hernia repair include closure of the defect, use of higher DIS class meshes, increased mesh overlap and additional fixation. In the clinical routine, all measures must be adapted to the individual tissue quality.
Conclusions
Using the conception of GRIP as the gained resistance towards pressure related impacts, a durable hernia repair can be designed from coefficients determined with a bench test or with computerized tomography of the human abdominal wall. Pain levels and hernia recurrence rates can be reduced in incisional hernia repair when biomechanical principles are considered.
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Affiliation(s)
- Friedrich Kallinowski
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany, University Hospital Heidelberg, Heidelberg, Germany
| | - Yannique Ludwig
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Dominik Gutjahr
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Christian Gerhard
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Hannah Schulte-Hörmann
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Lena Krimmel
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Carolin Lesch
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Katharina Uhr
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Germany
| | - Philipp Lösel
- Interdisciplinary Center for Scientific Computing, Engineering Mathematics and Computing Laboratory, Heidelberg, Germany
| | - Samuel Voss
- Otto von Guericke University Magdeburg, Laboratory of Fluid Dynamics and Technical Flows, Magdeburg, Germany
| | - Vincent Heuveline
- Interdisciplinary Center for Scientific Computing, Engineering Mathematics and Computing Laboratory, Heidelberg, Germany
| | - Matthias Vollmer
- Hamburg University of Technology, Hamburg University of Technology, Biomechanics, Hamburg, Germany, Biomechanics, Hamburg, Germany
| | | | - Regine Nessel
- Klinikum Am Gesundbrunnen, General, Visceral and Pediatric Surgery, Heilbronn, Germany
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3
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Lesch C, Kallinowski F, Uhr K, Vollmer M, Gerhard C, Gutjahr D, Krimmel L, Ludwig Y. P054 REDUCTION OF FAILURE RATES AFTER INCISIONAL HERNIA REPAIR BY ADDING A PROPHYLACTIC MESH. Br J Surg 2021. [DOI: 10.1093/bjs/znab395.050] [Citation(s) in RCA: 2] [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] [Indexed: 11/14/2022]
Abstract
Abstract
Aim
“Can a mesh reduce failure rates after closure of a hernia defect?”
Material and Methods
“Porcine abdominal walls and bovine flanks were used as model tissues. After preparation, a 15 cm long incision was placed in the linea alba of the porcine abdominal wall. An additional round 5 cm defect was punched in the middle of the incision. The bovine flank was prepared in a similar manner.
The incisions with the defects were closed with running sutures in a small stitch, small bite technique. Monomax® 2-0 sutures were used with suture to wound lengths above 4:1.
Dynamesh® CiCAT meshes of three different sizes were placed in the sublay position.
The mesh-tissue compounds were investigated on our self-built hydraulic bench test simulating coughs. Dynamic intermitted strain (DIS) was repeatedly delivered with impacts around 210 mmHg. Each of ten preparation was loaded 425 times by the pressure peaks.”
Results
“Small stitch, small bite sutures using 2-0 Monomax® with a suture-incision-ratio of 4.5:1 can provide a durable defect closure. Under other conditions, suture lines can reopen. A mesh reduces the recurrence of incisional hernia depending on the mesh size.”
Conclusions
“An additional DIS-class A mesh in sublay position can provide sufficient support for a suture closing the defect of the abdominal wall. It can prevent a tear-out of the suture from the tissue. On average, a mesh-augmented defect closure reduces the recurrence rate of incisional hernia.”
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Affiliation(s)
- Carolin Lesch
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Friedrich Kallinowski
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Uhr
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Matthias Vollmer
- Hamburg University of Technology, Hamburg University of Technology, Biomechanics, Hamburg, Germany, Biomechanics, Hamburg, Germany
| | - Christian Gerhard
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Dominik Gutjahr
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Lena Krimmel
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
| | - Yannique Ludwig
- University Hospital Heidelberg, General, Visceral and Transplantation Surgery, University Hospital Heidelberg, General, Visceral and Transplantation Surgery, Heidelberg, Germany
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4
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Kallinowski F, Ludwig Y, Gutjahr D, Gerhard C, Schulte-Hörmann H, Krimmel L, Lesch C, Uhr K, Lösel P, Voß S, Heuveline V, Vollmer M, Görich J, Nessel R. Biomechanical Influences on Mesh-Related Complications in Incisional Hernia Repair. Front Surg 2021; 8:763957. [PMID: 34778367 PMCID: PMC8586217 DOI: 10.3389/fsurg.2021.763957] [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: 08/24/2021] [Accepted: 09/30/2021] [Indexed: 11/13/2022] Open
Abstract
Aim: Hernia repair strengthens the abdominal wall with a textile mesh. Recurrence and pain indicate weak bonds between mesh and tissue. It remains a question which biomechanical factors strengthen the mesh-tissue interface, and whether surgeons can enhance the bond between mesh and tissue. Material and Methods: This study assessed the strength of the mesh-tissue interface by dynamic loads. A self-built bench test delivered dynamic impacts. The test simulated coughing. Porcine and bovine tissue were used for the bench test. Tissue quality, mesh adhesiveness, and fixation intensity influenced the retention power. The influences were condensed in a formula to assess the durability of the repair. The formula was applied to clinical work. The relative strength of reconstruction was related to the individual human abdominal wall. From computerized tomography at rest and during Valsalva's Maneuver, the tissue quality of the individual patient was determined before surgery. Results: The results showed that biomechanical parameters observed in porcine, bovine, and human tissue were in the same range. Tissues failed in distinct patterns. Sutures slackened or burst at vulnerable points. Both the load duration and the peak load increased destruction. Stress concentrations elevated failure rates. Regional areas of force contortions increased stress concentrations. Hernia repair improved strain levels. Measures for improvement included the closure of the defect, use of higher dynamic intermittent strain (DIS) class meshes, increased mesh overlap, and additional fixation. Surgeons chose the safety margin of the reconstruction as desired. Conclusion: The tissue quality has now been introduced into the concept of a critical and a gained resistance toward pressure-related impacts. A durable hernia repair could be designed from available coefficients. Using biomechanical principles, surgeons could minimize pain levels. Mesh-related complications such as hernia recurrence can potentially be avoided in incisional hernia repair.
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Affiliation(s)
- Friedrich Kallinowski
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Yannique Ludwig
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Dominik Gutjahr
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Christian Gerhard
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Hannah Schulte-Hörmann
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Lena Krimmel
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Carolin Lesch
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Katharina Uhr
- General, Visceral and Transplantation Surgery, University Hospital Heidelberg, Heidelberg, Germany
| | - Philipp Lösel
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing, Heidelberg, Germany
| | - Samuel Voß
- Laboratory of Fluid Dynamics and Technical Flows, Otto-von-Guericke University Magdeburg, Magdeburg, Germany
| | - Vincent Heuveline
- Engineering Mathematics and Computing Lab (EMCL), Interdisciplinary Center for Scientific Computing, Heidelberg, Germany
| | - Matthias Vollmer
- Biomechanics, Hamburg University of Technology, Hamburg, Germany
| | | | - Regine Nessel
- General, Visceral and Pediatric Surgery, Klinikum Am Gesundbrunnen, Heilbronn, Germany
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5
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Uhr K, Prager-van der Smissen WJC, Heine AAJ, Ozturk B, van Jaarsveld MTM, Boersma AWM, Jager A, Wiemer EAC, Smid M, Foekens JA, Martens JWM. MicroRNAs as possible indicators of drug sensitivity in breast cancer cell lines. PLoS One 2019; 14:e0216400. [PMID: 31063487 PMCID: PMC6504094 DOI: 10.1371/journal.pone.0216400] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2018] [Accepted: 04/20/2019] [Indexed: 12/20/2022] Open
Abstract
MicroRNAs (miRNAs) regulate gene expression post-transcriptionally. In this way they might influence whether a cell is sensitive or resistant to a certain drug. So far, only a limited number of relatively small scale studies comprising few cell lines and/or drugs have been performed. To obtain a broader view on miRNAs and their association with drug response, we investigated the expression levels of 411 miRNAs in relation to drug sensitivity in 36 breast cancer cell lines. For this purpose IC50 values of a drug screen involving 34 drugs were associated with miRNA expression data of the same breast cancer cell lines. Since molecular subtype of the breast cancer cell lines is considered a confounding factor in drug association studies, multivariate analysis taking subtype into account was performed on significant miRNA-drug associations which retained 13 associations. These associations consisted of 11 different miRNAs and eight different drugs (among which Paclitaxel, Docetaxel and Veliparib). The taxanes, Paclitaxel and Docetaxel, were the only drugs having miRNAs in common: hsa-miR-187-5p and hsa-miR-106a-3p indicative of drug resistance while Paclitaxel sensitivity alone associated with hsa-miR-556-5p. Tivantinib was associated with hsa-let-7d-5p and hsa-miR-18a-5p for sensitivity and hsa-miR-637 for resistance. Drug sensitivity was associated with hsa-let-7a-5p for Bortezomib, hsa-miR-135a-3p for JNJ-707 and hsa-miR-185-3p for Panobinostat. Drug resistance was associated with hsa-miR-182-5p for Veliparib and hsa-miR-629-5p for Tipifarnib. Pathway analysis for significant miRNAs was performed to reveal biological roles, aiding to find a potential mechanistic link for the observed associations with drug response. By doing so hsa-miR-187-5p was linked to the cell cycle G2-M checkpoint in line with this checkpoint being the target of taxanes. In conclusion, our study shows that miRNAs could potentially serve as biomarkers for intrinsic drug resistance and that pathway analyses can provide additional information in this context.
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Affiliation(s)
- Katharina Uhr
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Wendy J. C. Prager-van der Smissen
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Anouk A. J. Heine
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Bahar Ozturk
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marijn T. M. van Jaarsveld
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Antonius W. M. Boersma
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Agnes Jager
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Erik A. C. Wiemer
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - Marcel Smid
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John A. Foekens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
| | - John W. M. Martens
- Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Rotterdam, The Netherlands
- * E-mail:
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6
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Smid M, Wilting SM, Uhr K, Rodríguez-González FG, de Weerd V, Prager-Van der Smissen WJC, van der Vlugt-Daane M, van Galen A, Nik-Zainal S, Butler A, Martin S, Davies HR, Staaf J, van de Vijver MJ, Richardson AL, MacGrogan G, Salgado R, van den Eynden GGGM, Purdie CA, Thompson AM, Caldas C, Span PN, Sweep FCGJ, Simpson PT, Lakhani SR, Van Laere S, Desmedt C, Paradiso A, Eyfjord J, Broeks A, Vincent-Salomon A, Futreal AP, Knappskog S, King T, Viari A, Børresen-Dale AL, Stunnenberg HG, Stratton M, Foekens JA, Sieuwerts AM, Martens JWM. The circular RNome of primary breast cancer. Genome Res 2019; 29:356-366. [PMID: 30692147 PMCID: PMC6396421 DOI: 10.1101/gr.238121.118] [Citation(s) in RCA: 74] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 01/23/2019] [Indexed: 11/25/2022]
Abstract
Circular RNAs (circRNAs) are a class of RNAs that is under increasing scrutiny, although their functional roles are debated. We analyzed RNA-seq data of 348 primary breast cancers and developed a method to identify circRNAs that does not rely on unmapped reads or known splice junctions. We identified 95,843 circRNAs, of which 20,441 were found recurrently. Of the circRNAs that match exon boundaries of the same gene, 668 showed a poor or even negative (R < 0.2) correlation with the expression level of the linear gene. In silico analysis showed only a minority (8.5%) of circRNAs could be explained by known splicing events. Both these observations suggest that specific regulatory processes for circRNAs exist. We confirmed the presence of circRNAs of CNOT2, CREBBP, and RERE in an independent pool of primary breast cancers. We identified circRNA profiles associated with subgroups of breast cancers and with biological and clinical features, such as amount of tumor lymphocytic infiltrate and proliferation index. siRNA-mediated knockdown of circCNOT2 was shown to significantly reduce viability of the breast cancer cell lines MCF-7 and BT-474, further underlining the biological relevance of circRNAs. Furthermore, we found that circular, and not linear, CNOT2 levels are predictive for progression-free survival time to aromatase inhibitor (AI) therapy in advanced breast cancer patients, and found that circCNOT2 is detectable in cell-free RNA from plasma. We showed that circRNAs are abundantly present, show characteristics of being specifically regulated, are associated with clinical and biological properties, and thus are relevant in breast cancer.
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Affiliation(s)
- Marcel Smid
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Saskia M Wilting
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Katharina Uhr
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - F Germán Rodríguez-González
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Vanja de Weerd
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Wendy J C Prager-Van der Smissen
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Michelle van der Vlugt-Daane
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Anne van Galen
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Serena Nik-Zainal
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
- East Anglian Medical Genetics Service, Cambridge University Hospitals NHS Foundation Trust, Cambridge CB2 9NB, United Kingdom
| | - Adam Butler
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Sancha Martin
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Helen R Davies
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - Johan Staaf
- Division of Oncology and Pathology, Department of Clinical Sciences Lund, Lund University, SE-223 81 Lund, Sweden
| | - Marc J van de Vijver
- Department of Pathology, Academic Medical Center, 1105AZ Amsterdam, the Netherlands
| | - Andrea L Richardson
- Department of Pathology, Brigham and Women's Hospital, Boston, Massachusetts 02115, USA
- Dana-Farber Cancer Institute, Boston, Massachusetts 02215, USA
| | - Gaëten MacGrogan
- Département de Biopathologie, Institut Bergonié, CS 61283 33076 Bordeaux, France
| | - Roberto Salgado
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, B-1000 Brussels, Belgium
- Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium
| | - Gert G G M van den Eynden
- Department of Pathology/TCRU GZA, 2610 Antwerp, Belgium
- Molecular Immunology Unit, Jules Bordet Institute, B-1000 Brussels, Belgium
| | - Colin A Purdie
- Department of Pathology, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
| | - Alastair M Thompson
- Department of Pathology, Ninewells Hospital and Medical School, Dundee DD1 9SY, United Kingdom
| | - Carlos Caldas
- Cancer Research UK Cambridge Institute, University of Cambridge, Cambridge CB2 0RE, United Kingdom
| | - Paul N Span
- Department of Radiation Oncology, and Department of Laboratory Medicine, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Fred C G J Sweep
- Department of Laboratory Medicine, Radboud University Medical Center, 6525GA Nijmegen, the Netherlands
| | - Peter T Simpson
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, 4029 Brisbane, Australia
| | - Sunil R Lakhani
- Centre for Clinical Research, Faculty of Medicine, The University of Queensland, 4029 Brisbane, Australia
- Pathology Queensland, The Royal Brisbane and Women's Hospital, 4029 Brisbane, Australia
| | - Steven Van Laere
- Center for Oncological Research, University of Antwerp, 2610 Antwerp, Belgium
| | - Christine Desmedt
- Breast Cancer Translational Research Laboratory, Université Libre de Bruxelles, Institut Jules Bordet, B-1000 Brussels, Belgium
| | | | - Jorunn Eyfjord
- Cancer Research Laboratory, Faculty of Medicine, University of Iceland, 101 Reykjavik, Iceland
| | - Annegien Broeks
- The Netherlands Cancer Institute, 1066CX Amsterdam, the Netherlands
| | - Anne Vincent-Salomon
- Institut Curie, Department of Pathology and INSERM U934, 75248 Paris Cedex 05, France
| | - Andrew P Futreal
- Department of Genomic Medicine, University of Texas MD Anderson Cancer Center, Houston, Texas 77230, USA
| | - Stian Knappskog
- Department of Clinical Science, University of Bergen, 5020 Bergen, Norway
- Department of Oncology, Haukeland University Hospital, 5021 Bergen, Norway
| | - Tari King
- Memorial Sloan Kettering Cancer Center, New York, New York 10065, USA
| | - Alain Viari
- Synergie Lyon Cancer, Centre Léon Bérard, Lyon Cedex 08, France
- Equipe Erable, INRIA Grenoble-Rhône-Alpes, 38330 Montbonnot-Saint Martin, France
| | - Anne-Lise Børresen-Dale
- Department of Cancer Genetics, Institute for Cancer Research, Oslo University Hospital, The Norwegian Radiumhospital, 0310 Oslo, Norway
- K.G. Jebsen Centre for Breast Cancer Research, Institute for Clinical Medicine, University of Oslo, 0310 Oslo, Norway
| | - Hendrik G Stunnenberg
- Department of Molecular Biology, Faculty of Science, Radboud Institute for Molecular Life Sciences, Radboud University Nijmegen, 6525GA Nijmegen, the Netherlands
| | - Mike Stratton
- Wellcome Trust Sanger Institute, Hinxton, Cambridge CB10 1SA, United Kingdom
| | - John A Foekens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - Anieta M Sieuwerts
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
| | - John W M Martens
- Erasmus MC Cancer Institute and Cancer Genomics Netherlands, University Medical Center Rotterdam, Department of Medical Oncology, 3015GD Rotterdam, the Netherlands
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7
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Uhr K, Sieuwerts AM, de Weerd V, Smid M, Hammerl D, Foekens JA, Martens JWM. Association of microRNA-7 and its binding partner CDR1-AS with the prognosis and prediction of 1 st-line tamoxifen therapy in breast cancer. Sci Rep 2018; 8:9657. [PMID: 29941867 PMCID: PMC6018428 DOI: 10.1038/s41598-018-27987-w] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [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: 03/01/2018] [Accepted: 06/12/2018] [Indexed: 12/12/2022] Open
Abstract
The large number of non-coding RNAs (ncRNAs) and their breadth of functionalities has fuelled many studies on their roles in cancer. We previously linked four microRNAs to breast cancer prognosis. One of these microRNAs, hsa-miR-7, was found to be regulated by another type of ncRNA, the circular non-coding RNA (circRNA) CDR1-AS, which contains multiple hsa-miR-7 binding sites. Based on this finding, we studied the potential clinical value of this circRNA on breast cancer prognosis in a cohort based on a cohort that was previously analysed for hsa-miR-7 and in an adjuvant hormone-naïve cohort for 1st-line tamoxifen treatment outcomes, in which we also analysed hsa-miR-7. A negative correlation was observed between hsa-miR-7 and CDR1-AS in both cohorts. Despite associations with various clinical metrics (e.g., tumour grade, tumour size, and relapse location), CDR1-AS was neither prognostic nor predictive of relevant outcomes in our cohorts. However, we did observe stromal CDR1-AS expression, suggesting a possible cell-type specific interaction. Next to the known association of hsa-miR-7 expression with poor prognosis in primary breast cancer, we found that high hsa-miR-7 expression was predictive of an adverse response to tamoxifen therapy and poor progression-free and post-relapse overall survival in patients with recurrent disease.
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Affiliation(s)
- K Uhr
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - A M Sieuwerts
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands.
| | - V de Weerd
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - M Smid
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - D Hammerl
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J A Foekens
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
| | - J W M Martens
- Erasmus MC Cancer Institute, Erasmus University Medical Centre, Department of Medical Oncology and Cancer Genomics, Wytemaweg 80, 3015 CN, Rotterdam, The Netherlands
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Uhr K, Prager-van der Smissen WJC, Heine AAJ, Ozturk B, Smid M, Göhlmann HWH, Jager A, Foekens JA, Martens JWM. Understanding drugs in breast cancer through drug sensitivity screening. Springerplus 2015; 4:611. [PMID: 26543746 PMCID: PMC4628005 DOI: 10.1186/s40064-015-1406-8] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/29/2015] [Accepted: 10/06/2015] [Indexed: 01/18/2023]
Abstract
With substantial numbers of breast tumors showing or acquiring treatment resistance, it is of utmost importance to develop new agents for the treatment of the disease, to know their effectiveness against breast cancer and to understand their relationships with other drugs to best assign the right drug to the right patient. To achieve this goal drug screenings on breast cancer cell lines are a promising approach. In this study a large-scale drug screening of 37 compounds was performed on a panel of 42 breast cancer cell lines representing the main breast cancer subtypes. Clustering, correlation and pathway analyses were used for data analysis. We found that compounds with a related mechanism of action had correlated IC50 values and thus grouped together when the cell lines were hierarchically clustered based on IC50 values. In total we found six clusters of drugs of which five consisted of drugs with related mode of action and one cluster with two drugs not previously connected. In total, 25 correlated and four anti-correlated drug sensitivities were revealed of which only one drug, Sirolimus, showed significantly lower IC50 values in the luminal/ERBB2 breast cancer subtype. We found expected interactions but also discovered new relationships between drugs which might have implications for cancer treatment regimens.
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Affiliation(s)
- Katharina Uhr
- />Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Postbus 2040, ‘s-Gravendijkwal 230, 3000 CA Rotterdam, The Netherlands
| | - Wendy J. C. Prager-van der Smissen
- />Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Postbus 2040, ‘s-Gravendijkwal 230, 3000 CA Rotterdam, The Netherlands
| | - Anouk A. J. Heine
- />Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Postbus 2040, ‘s-Gravendijkwal 230, 3000 CA Rotterdam, The Netherlands
| | - Bahar Ozturk
- />Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Postbus 2040, ‘s-Gravendijkwal 230, 3000 CA Rotterdam, The Netherlands
| | - Marcel Smid
- />Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Postbus 2040, ‘s-Gravendijkwal 230, 3000 CA Rotterdam, The Netherlands
| | - Hinrich W. H. Göhlmann
- />Division of Janssen Pharmaceutica, Johnson & Johnson Pharmaceutical Research and Development, Turnhoutseweg 30, 2340 Beerse, Belgium
| | - Agnes Jager
- />Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Postbus 2040, ‘s-Gravendijkwal 230, 3000 CA Rotterdam, The Netherlands
| | - John A. Foekens
- />Department of Medical Oncology, Erasmus MC Cancer Institute, Erasmus University Medical Center, Postbus 2040, ‘s-Gravendijkwal 230, 3000 CA Rotterdam, The Netherlands
| | - John W. M. Martens
- />Department of Medical Oncology and Cancer Genomics Netherlands, Erasmus MC Cancer Institute, Erasmus University Medical Center, Postbus 2040, ‘s-Gravendijkwal 230, 3000 CA Rotterdam, The Netherlands
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Teumer A, Ernst FD, Wiechert A, Uhr K, Nauck M, Petersmann A, Völzke H, Völker U, Homuth G. Comparison of genotyping using pooled DNA samples (allelotyping) and individual genotyping using the affymetrix genome-wide human SNP array 6.0. BMC Genomics 2013; 14:506. [PMID: 23885805 PMCID: PMC3727995 DOI: 10.1186/1471-2164-14-506] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [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: 12/19/2012] [Accepted: 07/23/2013] [Indexed: 12/26/2022] Open
Abstract
Background Genome-wide association studies (GWAS) using array-based genotyping technology are widely used to identify genetic loci associated with complex diseases or other phenotypes. The costs of GWAS projects based on individual genotyping are still comparatively high and increase with the size of study populations. Genotyping using pooled DNA samples, as also being referred as to allelotyping approach, offers an alternative at affordable costs. In the present study, data from 100 DNA samples individually genotyped with the Affymetrix Genome-Wide Human SNP Array 6.0 were used to estimate the error of the pooling approach by comparing the results with those obtained using the same array type but DNA pools each composed of 50 of the same samples. Newly developed and established methods for signal intensity correction were applied. Furthermore, the relative allele intensity signals (RAS) obtained by allelotyping were compared to the corresponding values derived from individual genotyping. Similarly, differences in RAS values between pools were determined and compared. Results Regardless of the intensity correction method applied, the pooling-specific error of the pool intensity values was larger for single pools than for the comparison of the intensity values of two pools, which reflects the scenario of a case–control study. Using 50 pooled samples and analyzing 10,000 SNPs with a minor allele frequency of >1% and applying the best correction method for the corresponding type of comparison, the 90% quantile (median) of the pooling-specific absolute error of the RAS values for single sub-pools and the SNP-specific difference in allele frequency comparing two pools was 0.064 (0.026) and 0.056 (0.021), respectively. Conclusions Correction of the RAS values reduced the error of the RAS values when analyzing single pool intensities. We developed a new correction method with high accuracy but low computational costs. Correction of RAS, however, only marginally reduced the error of true differences between two sample groups and those obtained by allelotyping. Exclusion of SNPs with a minor allele frequency of ≤1% notably reduced the pooling-specific error. Our findings allow for improving the estimation of the pooling-specific error and may help in designing allelotyping studies using the Affymetrix Genome-Wide Human SNP Array 6.0.
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Affiliation(s)
- Alexander Teumer
- Interfaculty Institute for Genetics and Functional Genomics, University Medicine Greifswald, 17487 Greifswald, Germany.
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Ernst FD, Uhr K, Teumer A, Fanghänel J, Schulz S, Noack B, Gonzales J, Reichert S, Eickholz P, Holtfreter B, Meisel P, Linden GJ, Homuth G, Kocher T. Replication of the association of chromosomal region 9p21.3 with generalized aggressive periodontitis (gAgP) using an independent case-control cohort. BMC Med Genet 2010; 11:119. [PMID: 20696043 PMCID: PMC2924866 DOI: 10.1186/1471-2350-11-119] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2009] [Accepted: 08/09/2010] [Indexed: 12/21/2022]
Abstract
Background The human chromosomal region 9p21.3 has been shown to be strongly associated with Coronary Heart Disease (CHD) in several Genome-wide Association Studies (GWAS). Recently, this region has also been shown to be associated with Aggressive Periodontitis (AgP), strengthening the hypothesis that the established epidemiological association between periodontitis and CHD is caused by a shared genetic background, in addition to common environmental and behavioural risk factors. However, the size of the analyzed cohorts in this primary analysis was small compared to other association studies on complex diseases. Using our own AgP cohort, we attempted to confirm the described associations for the chromosomal region 9p21.3. Methods We analyzed our cohort consisting of patients suffering from the most severe form of AgP, generalized AgP (gAgP) (n = 130) and appropriate periodontally healthy control individuals (n = 339) by genotyping four tagging SNPs (rs2891168, rs1333042, rs1333048 and rs496892), located in the chromosomal region 9p21.3, that have been associated with AgP. Results The results confirmed significant associations between three of the four SNPs and gAgP. The combination of our results with those from the study which described this association for the first time in a meta-analysis of the four tagging SNPs produced clearly lower p-values compared with the results of each individual study. According to these results, the most plausible genetic model for the association of all four tested SNPs with gAgP seems to be the multiplicative one. Conclusion We positively replicated the finding of an association between the chromosomal region 9p21.3 and gAgP. This result strengthens support for the hypothesis that shared susceptibility genes within this chromosomal locus might be involved in the pathogenesis of both CHD and gAgP.
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Affiliation(s)
- Florian D Ernst
- Interfaculty Institute for Genetics and Functional Genomics, Department of Functional Genomics, Ernst-Moritz-Arndt-University Greifswald, Greifswald, Germany
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