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Boutros M, Baumann M, Bigas A, Chaabane L, Guérin J, Habermann JK, Jobard A, Pelicci PG, Stegle O, Tonon G, Valencia A, Winkler EC, Blanc P, De Maria R, Medema RH, Nagy P, Tabernero J, Solary E. UNCAN.eu: Toward a European Federated Cancer Research Data Hub. Cancer Discov 2024; 14:30-35. [PMID: 38213296 PMCID: PMC10784740 DOI: 10.1158/2159-8290.cd-23-1111] [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: 01/13/2024]
Abstract
To enable a collective effort that generates a new level of UNderstanding CANcer (UNCAN.eu) [Cancer Discov (2022) 12 (11): OF1], the European Union supports the creation of a sustainable platform that connects cancer research across Member States. A workshop hosted in Heidelberg gathered European cancer experts to identify ongoing initiatives that may contribute to building this platform and discuss the governance and long-term evolution of a European Federated Cancer Data Hub.
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Affiliation(s)
- Michael Boutros
- German Cancer Research Center (DKFZ), Division of Signaling and Functional Genomics and Heidelberg University, Medical Faculty Heidelberg, Institute for Human Genetics, Heidelberg, Germany
| | | | - Anna Bigas
- Centro de Investigación Biomedica en Red-Oncología (CIBERONC), Instituto de Salud Carlos III, Madrid, Spain
| | - Linda Chaabane
- Euro-BioImaging ERIC, Med-Hub, National Research Council of Italy (CNR), Turin, Italy
| | | | - Jens K. Habermann
- Interdisciplinary Center for Biobanking-Lübeck (ICB-L), University of Lübeck, Lübeck, Germany
| | - Aurélien Jobard
- Institut National du Cancer (INCa), Boulogne Billancourt, France
| | - Pier Giuseppe Pelicci
- Department of Experimental Oncology, IEO European Institute of Oncology IRCCS, Milano, Italy
| | - Oliver Stegle
- DKFZ, Division of Computational Genomics and Systems Genetics, Heidelberg, Germany
- Genome Biology Unit, European Molecular Biology, Heidelberg, Germany
| | - Giovanni Tonon
- Center for Omics Sciences, IRCCS San Raffaele Scientific Institute, Milan, Italy
| | - Alfonso Valencia
- Barcelona Supercomputing Center, Catalan Institution for Research and Advanced Studies (ICREA), Barcelona, Spain
| | - Eva C. Winkler
- National Center for Tumor Diseases (NCT), Heidelberg University, Section Translational Medical Ethics, Heidelberg, Germany
| | | | - Ruggero De Maria
- Fondazione Policlinico Universitario A. Gemelli IRCCS, Università Cattolica del Sacro Cuore, Rome, Italy
| | - Rene H. Medema
- Oncode Institute and The Netherlands Cancer Institute, Amsterdam, the Netherlands
| | - Peter Nagy
- National Institute of Oncology and the National Tumor Biology Laboratory, Budapest, Department of Anatomy and Histology, HUN-REN–UVMB Laboratory of Redox Biology Research Group, University of Veterinary Medicine, and Chemistry Institute, University of Debrecen, Debrecen, Hungary
| | - Josep Tabernero
- DKFZ, Division of Computational Genomics and Systems Genetics, Heidelberg, Germany
- Vall d'Hebron Hospital Campus & Institute of Oncology (VHIO), Barcelona, Spain
| | - Eric Solary
- Université Paris-Saclay and INSERM, Gustave Roussy Cancer Center, Villejuif, France
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2
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Praus F, Künstner A, Sauer T, Kohl M, Kern K, Deichmann S, Végvári Á, Keck T, Busch H, Habermann JK, Gemoll T. Panomics reveals patient individuality as the major driver of colorectal cancer progression. J Transl Med 2023; 21:41. [PMID: 36691026 PMCID: PMC9869555 DOI: 10.1186/s12967-022-03855-0] [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] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2022] [Accepted: 12/26/2022] [Indexed: 01/24/2023] Open
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most prevalent cancers, with over one million new cases per year. Overall, prognosis of CRC largely depends on the disease stage and metastatic status. As precision oncology for patients with CRC continues to improve, this study aimed to integrate genomic, transcriptomic, and proteomic analyses to identify significant differences in expression during CRC progression using a unique set of paired patient samples while considering tumour heterogeneity. METHODS We analysed fresh-frozen tissue samples prepared under strict cryogenic conditions of matched healthy colon mucosa, colorectal carcinoma, and liver metastasis from the same patients. Somatic mutations of known cancer-related genes were analysed using Illumina's TruSeq Amplicon Cancer Panel; the transcriptome was assessed comprehensively using Clariom D microarrays. The global proteome was evaluated by liquid chromatography-coupled mass spectrometry (LC‒MS/MS) and validated by two-dimensional difference in-gel electrophoresis. Subsequent unsupervised principal component clustering, statistical comparisons, and gene set enrichment analyses were calculated based on differential expression results. RESULTS Although panomics revealed low RNA and protein expression of CA1, CLCA1, MATN2, AHCYL2, and FCGBP in malignant tissues compared to healthy colon mucosa, no differentially expressed RNA or protein targets were detected between tumour and metastatic tissues. Subsequent intra-patient comparisons revealed highly specific expression differences (e.g., SRSF3, OLFM4, and CEACAM5) associated with patient-specific transcriptomes and proteomes. CONCLUSION Our research results highlight the importance of inter- and intra-tumour heterogeneity as well as individual, patient-paired evaluations for clinical studies. In addition to changes among groups reflecting CRC progression, we identified significant expression differences between normal colon mucosa, primary tumour, and liver metastasis samples from individuals, which might accelerate implementation of precision oncology in the future.
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Affiliation(s)
- Friederike Praus
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Axel Künstner
- Medical Systems Biology Group, Lübeck Institute Für Experimental Dermatology, University of Lübeck, Campus Lübeck, 23538, Lübeck, Germany
| | - Thorben Sauer
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Michael Kohl
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Medical Systems Biology Group, Lübeck Institute Für Experimental Dermatology, University of Lübeck, Campus Lübeck, 23538, Lübeck, Germany
| | - Katharina Kern
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Steffen Deichmann
- Department of Surgery, University Hospital Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Ákos Végvári
- Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
- Proteomics Biomedicum, Division of Physiological Chemistry I, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, 171 77, Stockholm, Sweden
| | - Tobias Keck
- Department of Surgery, University Hospital Schleswig-Holstein, Campus Lübeck, 23538, Lübeck, Germany
| | - Hauke Busch
- Medical Systems Biology Group, Lübeck Institute Für Experimental Dermatology, University of Lübeck, Campus Lübeck, 23538, Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
- Department of Oncology Pathology, Karolinska Institutet, 171 64, Solna, Sweden
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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Lange T, Valentiner U, Wicklein D, Maar H, Labitzky V, Ahlers AK, Starzonek S, Genduso S, Staffeldt L, Pahlow C, Dück AM, Stürken C, Baranowsky A, Bauer AT, Bulk E, Schwab A, Riecken K, Börnchen C, Kiefmann R, Abraham V, DeLisser HM, Gemoll T, Habermann JK, Block A, Pantel K, Schumacher U. Tumor cell E-selectin ligands determine partialefficacy of bortezomib on spontaneous lung metastasis formation of solid human tumors in vivo. Mol Ther 2022; 30:1536-1552. [PMID: 35031433 PMCID: PMC9077315 DOI: 10.1016/j.ymthe.2022.01.017] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [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: 10/21/2021] [Revised: 12/21/2021] [Accepted: 01/10/2022] [Indexed: 10/19/2022] Open
Abstract
Extravasation of circulating tumor cells (CTCs) is critical for metastasis and is initiated by adhesive interactions between glycoligands on CTCs and E-selectin on endothelia. Here, we show that the clinically approved proteasome inhibitor bortezomib (BZM; Velcade) counteracts the cytokine-dependent induction of E-selectin in the lung mediated by the primary tumor, thereby impairing endothelial adhesion and thus spontaneous lung metastasis in vivo. However, the efficacy of BZM crucially depends on the tumor cells' E-selectin ligands, which determine distinct adhesion patterns. The canonical ligands sialyl-Lewis A (sLeA) and sLeX mediate particularly high-affinity E-selectin binding so that the incomplete E-selectin-reducing effect of BZM is not sufficient to disrupt adhesion or metastasis. In contrast, tumor cells lacking sLeA/X nevertheless bind E-selectin, but with low affinity, so that adhesion and lung metastasis are significantly diminished. Such low-affinity E-selectin ligands apparently consist of sialylated MGAT5 products on CD44. BZM no longer has anti-metastatic activity after CD44 knockdown in sLeA/X-negative tumor cells or E-selectin knockout in mice. sLeA/X can be determined by immunohistochemistry in cancer samples, which might aid patient stratification. These data suggest that BZM might act as a drug for inhibiting extravasation and thus distant metastasis formation in malignancies expressing low-affinity E-selectin ligands.
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Affiliation(s)
- Tobias Lange
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany.
| | - Ursula Valentiner
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Daniel Wicklein
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Hanna Maar
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Vera Labitzky
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Ann-Kristin Ahlers
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sarah Starzonek
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Sandra Genduso
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Lisa Staffeldt
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Carolin Pahlow
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anna-Maria Dück
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christine Stürken
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Anke Baranowsky
- Department of Trauma and Orthopedic Surgery, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Alexander T Bauer
- Department of Dermatology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Etmar Bulk
- Institute of Physiology II, University of Münster, 48149 Münster, Germany
| | - Albrecht Schwab
- Institute of Physiology II, University of Münster, 48149 Münster, Germany
| | - Kristoffer Riecken
- Research Department Cell and Gene Therapy, Department of Stem Cell Transplantation, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Christian Börnchen
- Department of Anesthesiology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Rainer Kiefmann
- Department of Anesthesiology, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Valsamma Abraham
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA
| | - Horace M DeLisser
- Pulmonary, Allergy and Critical Care Division, Department of Medicine, School of Medicine, University of Pennsylvania, Philadelphia, PA 19104-4539, USA
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig Holstein, Campus Lübeck, 23538 Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig Holstein, Campus Lübeck, 23538 Lübeck, Germany
| | - Andreas Block
- Department of Oncology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Klaus Pantel
- Institute of Tumor Biology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
| | - Udo Schumacher
- Institute of Anatomy and Experimental Morphology, University Cancer Center Hamburg, University Medical Center Hamburg-Eppendorf, 20246 Hamburg, Germany
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Nießen L, Facchinetti G, Elsner T, Wendlandt R, Gemoll T, Habermann JK, Schulz AP. Effect of volume flows on the viability of MSCs during injection through a cannula. Current Directions in Biomedical Engineering 2021. [DOI: 10.1515/cdbme-2021-2069] [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: 11/15/2022] Open
Abstract
Abstract
Introduction: Clinical trials currently evaluate the use of mesenchymal stem cells (MSCs) for the treatment of non-union bone fractures. The stem cells are injected directly into the non-union area of a bone via a cannula. During this injection process, pressure and shear forces affect the MSCs which could influence the viability of the cells. One parameter that influences the level of the shear forces is the volume flow. The aim of this study is to show whether the injection process with two different volume flows influences the cell viability. Methods: MSCs were isolated from bone tissue, harvested during arthroplasty. Afterwards, they were diluted to a concentration of 1 million cells/mL and 1 mL of this suspension was injected through a cannula with 200 mm length and 2 mm diameter (14 G) with volume flows of 38 and 100 mL/min. The evaluation was performed by detecting living, apoptotic, and dead cells using flow cytometry. The statistical analysis was performed with a Kruskal-Wallis-test to identify significant differences and with a TOST procedure for significant equivalence. The significance level was set to 5 % and the equivalence margin to 20 %. Results: The cell population of healthy cells was in the control group 85.88±2.98 %. After an injection with 38 mL/min the population of healthy cells was 86.04±2.53 % and with 100 ml/min 85.48±1.64 %. The statistical analysis revealed no significant difference between these groups (p = 0.99), but a significant equivalence between the control group and the two volume flows (38 mL/min: p = 0.002, 100 mL/min: p = 0.001). In addition the results show no increase of apoptotic and dead cells in the population after injection. Conclusion: The results indicate that the injection process through the cannula with these volume flows has no effect on the viability of the MSCs.
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Affiliation(s)
- Lina Nießen
- Department for orthopaedic and trauma surgery, University Hospital Schleswig-Holstein, and Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering, Lübeck , Germany
| | - Giulia Facchinetti
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig- Holstein, Lübeck , Germany
| | - Till Elsner
- University Lübeck, MINT Section, Lübeck , Germany
| | - Robert Wendlandt
- Department for orthopaedic and trauma surgery, University Hospital Schleswig-Holstein, Lübeck , Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig- Holstein, Lübeck , Germany
| | - Jens K. Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck , Germany
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck , Germany
| | - Arndt-Peter Schulz
- Fraunhofer Research Institution for Individualized and Cell-Based Medical Engineering, Lübeck, Germany and BG Unfallklinikum Hamburg, Department of Biomechatronics, Hamburg , Germany
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Liegmann AS, Heselmeyer-Haddad K, Lischka A, Hirsch D, Chen WD, Torres I, Gemoll T, Rody A, Thorns C, Gertz EM, Alkemade H, Hu Y, Habermann JK, Ried T. Single Cell Genetic Profiling of Tumors of Breast Cancer Patients Aged 50 Years and Older Reveals Enormous Intratumor Heterogeneity Independent of Individual Prognosis. Cancers (Basel) 2021; 13:3366. [PMID: 34282768 PMCID: PMC8267950 DOI: 10.3390/cancers13133366] [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] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/18/2021] [Revised: 06/25/2021] [Accepted: 06/30/2021] [Indexed: 02/07/2023] Open
Abstract
PURPOSE Older breast cancer patients are underrepresented in cancer research even though the majority (81.4%) of women dying of breast cancer are 55 years and older. Here we study a common phenomenon observed in breast cancer which is a large inter- and intratumor heterogeneity; this poses a tremendous clinical challenge, for example with respect to treatment stratification. To further elucidate genomic instability and tumor heterogeneity in older patients, we analyzed the genetic aberration profiles of 39 breast cancer patients aged 50 years and older (median 67 years) with either short (median 2.4 years) or long survival (median 19 years). The analysis was based on copy number enumeration of eight breast cancer-associated genes using multiplex interphase fluorescence in situ hybridization (miFISH) of single cells, and by targeted next-generation sequencing of 563 cancer-related genes. RESULTS We detected enormous inter- and intratumor heterogeneity, yet maintenance of common cancer gene mutations and breast cancer specific chromosomal gains and losses. The gain of COX2 was most common (72%), followed by MYC (69%); losses were most prevalent for CDH1 (74%) and TP53 (69%). The degree of intratumor heterogeneity did not correlate with disease outcome. Comparing the miFISH results of diploid with aneuploid tumor samples significant differences were found: aneuploid tumors showed significantly higher average signal numbers, copy number alterations (CNAs) and instability indices. Mutations in PIKC3A were mostly restricted to luminal A tumors. Furthermore, a significant co-occurrence of CNAs of DBC2/MYC, HER2/DBC2 and HER2/TP53 and mutual exclusivity of CNAs of HER2 and PIK3CA mutations and CNAs of CCND1 and PIK3CA mutations were revealed. CONCLUSION Our results provide a comprehensive picture of genome instability profiles with a large variety of inter- and intratumor heterogeneity in breast cancer patients aged 50 years and older. In most cases, the distribution of chromosomal aneuploidies was consistent with previous results; however, striking exceptions, such as tumors driven by exclusive loss of chromosomes, were identified.
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Affiliation(s)
- Anna-Sophie Liegmann
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Annette Lischka
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
| | - Daniela Hirsch
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
- Institute of Pathology, University Medical Center Mannheim, Medical Faculty Mannheim, Heidelberg University, 68167 Mannheim, Germany
| | - Wei-Dong Chen
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Irianna Torres
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Timo Gemoll
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
| | - Achim Rody
- Department of Gynecology and Obstetrics, Campus Lübeck, University Hospital of Schleswig-Holstein, 23562 Lübeck, Germany;
| | - Christoph Thorns
- Institute of Pathology, Marienkrankenhaus Hamburg, 22087 Hamburg, Germany;
- Institute of Pathology, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany
| | - Edward Michael Gertz
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA;
| | - Hendrik Alkemade
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
| | - Yue Hu
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
| | - Jens K. Habermann
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, 23562 Lübeck, Germany; (A.-S.L.); (A.L.); (T.G.); (H.A.)
- Department of Oncology-Pathology, Cancer Center Karolinska, Karolinska Institute, 171 77 Stockholm, Sweden
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA; (K.H.-H.); (D.H.); (W.-D.C.); (I.T.); (Y.H.)
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6
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Patkar S, Heselmeyer-Haddad K, Auslander N, Hirsch D, Camps J, Bronder D, Brown M, Chen WD, Lokanga R, Wangsa D, Wangsa D, Hu Y, Lischka A, Braun R, Emons G, Ghadimi BM, Gaedcke J, Grade M, Montagna C, Lazebnik Y, Difilippantonio MJ, Habermann JK, Auer G, Ruppin E, Ried T. Hard wiring of normal tissue-specific chromosome-wide gene expression levels is an additional factor driving cancer type-specific aneuploidies. Genome Med 2021; 13:93. [PMID: 34034815 PMCID: PMC8147418 DOI: 10.1186/s13073-021-00905-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [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: 01/05/2021] [Accepted: 05/06/2021] [Indexed: 12/12/2022] Open
Abstract
Background Many carcinomas have recurrent chromosomal aneuploidies specific to the tissue of tumor origin. The reason for this specificity is not completely understood. Methods In this study, we looked at the frequency of chromosomal arm gains and losses in different cancer types from the The Cancer Genome Atlas (TCGA) and compared them to the mean gene expression of each chromosome arm in corresponding normal tissues of origin from the Genotype-Tissue Expression (GTEx) database, in addition to the distribution of tissue-specific oncogenes and tumor suppressors on different chromosome arms. Results This analysis revealed a complex picture of factors driving tumor karyotype evolution in which some recurrent chromosomal copy number reflect the chromosome arm-wide gene expression levels of the their normal tissue of tumor origin. Conclusions We conclude that the cancer type-specific distribution of chromosomal arm gains and losses is potentially “hardwiring” gene expression levels characteristic of the normal tissue of tumor origin, in addition to broadly modulating the expression of tissue-specific tumor driver genes. Supplementary Information The online version contains supplementary material available at 10.1186/s13073-021-00905-y.
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Affiliation(s)
- Sushant Patkar
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Department of Computer Science, University of Maryland, College Park, USA
| | - Kerstin Heselmeyer-Haddad
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Noam Auslander
- Department of Computer Science, University of Maryland, College Park, USA.,National Center for Biotechnology Information, NIH, Bethesda, MD, 20892, USA
| | - Daniela Hirsch
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Jordi Camps
- Gastrointestinal and Pancreatic Oncology Team, Institut D'Investigacions Biomèdiques August Pi i Sunyer, (IDIBAPS), Hospital Clínic of Barcelona, CIBEREHD, 08036, Barcelona, Spain
| | - Daniel Bronder
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Markus Brown
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Wei-Dong Chen
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Rachel Lokanga
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Darawalee Wangsa
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Danny Wangsa
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Yue Hu
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Annette Lischka
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Rüdiger Braun
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Georg Emons
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.,Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - B Michael Ghadimi
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Jochen Gaedcke
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Marian Grade
- Department of General, Visceral and Pediatric Surgery, University Medical Center, Göttingen, Germany
| | - Cristina Montagna
- Department of Genetics and Pathology, Albert Einstein College of Medicine, Bronx, NY, USA
| | | | - Michael J Difilippantonio
- Division of Cancer Treatment and Diagnosis, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University Medical Center Schleswig Holstein, Campus Lübeck, Lübeck, Germany
| | - Gert Auer
- Department of Oncology and Pathology, CancerCenter Karolinska, Karolinska Institute and University Hospital, Stockholm, Sweden
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA
| | - Thomas Ried
- Section of Cancer Genomics, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, MD, 20892, USA.
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7
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Lischka A, Doberstein N, Freitag-Wolf S, Koçak A, Gemoll T, Heselmeyer-Haddad K, Ried T, Auer G, Habermann JK. Genome Instability Profiles Predict Disease Outcome in a Cohort of 4,003 Patients with Breast Cancer. Clin Cancer Res 2020; 26:4606-4615. [PMID: 32522886 DOI: 10.1158/1078-0432.ccr-20-0566] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [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] [Received: 02/13/2020] [Revised: 04/16/2020] [Accepted: 06/03/2020] [Indexed: 12/12/2022]
Abstract
PURPOSE The choice of therapy for patients with breast cancer is often based on clinicopathologic parameters, hormone receptor status, and HER2 amplification. To improve individual prognostication and tailored treatment decisions, we combined clinicopathologic prognostic data with genome instabilty profiles established by quantitative measurements of the DNA content. EXPERIMENTAL DESIGN We retrospectively assessed clinical data of 4,003 patients with breast cancer with a minimum postoperative follow-up period of 10 years. For the entire cohort, we established genome instability profiles. We applied statistical methods, including correlation matrices, Kaplan-Meier curves, and multivariable Cox proportional hazard models, to ascertain the potential of standard clinicopathologic data and genome instability profiles as independent predictors of disease-specific survival in distinct subgroups, defined clinically or with respect to treatment. RESULTS In Cox regression analyses, two parameters of the genome instability profiles, the S-phase fraction and the stemline scatter index, emerged as independent predictors in premenopausal women, outperforming all clinicopathologic parameters. In postmenopausal women, age and hormone receptor status were the predominant prognostic factors. However, by including S-phase fraction and 2.5c exceeding rate, we could improve disease outcome prediction in pT1 tumors irrespective of the lymph node status. In pT3-pT4 tumors, a higher S-phase fraction led to poorer prognosis. In patients who received adjuvant endocrine therapy, chemotherapy or radiotherapy, or a combination, the ploidy profiles improved prognostication. CONCLUSIONS Genome instability profiles predict disease outcome in patients with breast cancer independent of clinicopathologic parameters. This applies especially to premenopausal patients. In patients receiving adjuvant therapy, the profiles improve identification of high-risk patients.
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Affiliation(s)
- Annette Lischka
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Germany
| | - Natalie Doberstein
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Germany
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, Kiel University, University Hospital Schleswig-Holstein, Campus Kiel, Germany
| | - Ayla Koçak
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Germany
| | | | - Thomas Ried
- Genetics Branch, NCI, NIH, Bethesda, Maryland.
| | - Gert Auer
- Department of Pathology and Oncology, Karolinska University Hospital and Karolinska Institute, Stockholm, Sweden
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Germany
- Department of Pathology and Oncology, Karolinska University Hospital and Karolinska Institute, Stockholm, Sweden
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8
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Bartsch YC, Eschweiler S, Leliavski A, Lunding HB, Wagt S, Petry J, Lilienthal GM, Rahmöller J, de Haan N, Hölscher A, Erapaneedi R, Giannou AD, Aly L, Sato R, de Neef LA, Winkler A, Braumann D, Hobusch J, Kuhnigk K, Krémer V, Steinhaus M, Blanchard V, Gemoll T, Habermann JK, Collin M, Salinas G, Manz RA, Fukuyama H, Korn T, Waisman A, Yogev N, Huber S, Rabe B, Rose-John S, Busch H, Berberich-Siebelt F, Hölscher C, Wuhrer M, Ehlers M. IgG Fc sialylation is regulated during the germinal center reaction following immunization with different adjuvants. J Allergy Clin Immunol 2020; 146:652-666.e11. [PMID: 32445838 DOI: 10.1016/j.jaci.2020.04.059] [Citation(s) in RCA: 35] [Impact Index Per Article: 8.8] [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: 12/12/2019] [Revised: 04/23/2020] [Accepted: 04/24/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Effector functions of IgG Abs are regulated by their Fc N-glycosylation pattern. IgG Fc glycans that lack galactose and terminal sialic acid residues correlate with the severity of inflammatory (auto)immune disorders and have also been linked to protection against viral infection and discussed in the context of vaccine-induced protection. In contrast, sialylated IgG Abs have shown immunosuppressive effects. OBJECTIVE We sought to investigate IgG glycosylation programming during the germinal center (GC) reaction following immunization of mice with a foreign protein antigen and different adjuvants. METHODS Mice were analyzed for GC T-cell, B-cell, and plasma cell responses, as well as for antigen-specific serum IgG subclass titers and Fc glycosylation patterns. RESULTS Different adjuvants induce distinct IgG+ GC B-cell responses with specific transcriptomes and expression levels of the α2,6-sialyltransferase responsible for IgG sialylation that correspond to distinct serum IgG Fc glycosylation patterns. Low IgG Fc sialylation programming in GC B cells was overall highly dependent on the Foxp3- follicular helper T (TFH) cell-inducing cytokine IL-6, here in particular induced by water-in-oil adjuvants and Mycobacterium tuberculosis. Furthermore, low IgG Fc sialylation programming was dependent on adjuvants that induced IL-27 receptor-dependent IFN-γ+ TFH1 cells, IL-6/IL-23-dependent IL-17A+ TFH17 cells, and high ratios of TFH cells to Foxp3+ follicular regulatory T cells. Here, the 2 latter were dependent on M tuberculosis and its cord factor. CONCLUSION This study's findings regarding adjuvant-dependent GC responses and IgG glycosylation programming may aid in the development of novel vaccination strategies to induce IgG Abs with both high affinity and defined Fc glycosylation patterns in the GC.
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Affiliation(s)
- Yannic C Bartsch
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Simon Eschweiler
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Alexei Leliavski
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Hanna B Lunding
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Sander Wagt
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany; Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Janina Petry
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Gina-Maria Lilienthal
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Johann Rahmöller
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany; Department of Anesthesiology and Intensive Care, University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Noortje de Haan
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Raghu Erapaneedi
- Institute for Pathology, University of Würzburg, Würzburg, Germany
| | - Anastasios D Giannou
- First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Lilian Aly
- Department of Neurology, Technical University of Munich, Klinikum rechts der Isar, Germany
| | - Ryota Sato
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Louise A de Neef
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - André Winkler
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany; Laboratory of Tolerance and Autoimmunity at the German Rheumatism Research Center, a Leibniz Institute, Berlin, Germany
| | - Dominique Braumann
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany; Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Juliane Hobusch
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Kyra Kuhnigk
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Vanessa Krémer
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Moritz Steinhaus
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Véronique Blanchard
- Institute of Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-Universitätsmedizin Berlin, corporate member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Mattias Collin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Gabriela Salinas
- NGS-Integrative Genomics, Institute Human Genetics, University Medical Center Göttingen, Göttingen, Germany
| | - Rudolf A Manz
- Institute for Systemic Inflammation Research, University of Lübeck, Lübeck, Germany
| | - Hidehiro Fukuyama
- Laboratory for Lymphocyte Differentiation, RIKEN Center for Integrative Medical Sciences, Yokohama, Kanagawa, Japan
| | - Thomas Korn
- Department of Neurology, Technical University of Munich, Klinikum rechts der Isar, Germany; Munich Cluster for Systems Neurology, SyNergy, Germany
| | - Ari Waisman
- Institute for Molecular Medicine, University Medical Center of the Johannes Gutenberg-University Mainz, Mainz, Germany
| | - Nir Yogev
- Clinic and Polyclinic for Dermatology and Venerology, University Hospital Cologne, Cologne, Germany
| | - Samuel Huber
- First Department of Medicine, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Björn Rabe
- Institute of Biochemistry, Kiel University, Kiel, Germany
| | | | - Hauke Busch
- Lübeck Institute of Experimental Dermatology, University of Lübeck, Lübeck, Germany
| | - Friederike Berberich-Siebelt
- Institute for Pathology, University of Würzburg, Würzburg, Germany; Comprehensive Cancer Center Mainfranken, University of Würzburg, Würzburg, Germany
| | - Christoph Hölscher
- Infection Immunology, Research Center Borstel, Borstel, Germany; German Center for Infection Research, Partner Site Hamburg-Lübeck-Borstel-Riems, Borstel, Germany
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Marc Ehlers
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutritional Medicine, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany; Laboratory of Tolerance and Autoimmunity at the German Rheumatism Research Center, a Leibniz Institute, Berlin, Germany; Airway Research Center North, University of Lübeck, German Center for Lung Research, Lübeck, Germany.
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9
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Koçak A, Heselmeyer-Haddad K, Lischka A, Hirsch D, Fiedler D, Hu Y, Doberstein N, Torres I, Chen WD, Gertz EM, Schäffer AA, Freitag-Wolf S, Kirfel J, Auer G, Habermann JK, Ried T. High Levels of Chromosomal Copy Number Alterations and TP53 Mutations Correlate with Poor Outcome in Younger Breast Cancer Patients. Am J Pathol 2020; 190:1643-1656. [PMID: 32416097 DOI: 10.1016/j.ajpath.2020.04.015] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Revised: 04/08/2020] [Accepted: 04/27/2020] [Indexed: 12/20/2022]
Abstract
Prognosis in young patients with breast cancer is generally poor, yet considerable differences in clinical outcomes between individual patients exist. To understand the genetic basis of the disparate clinical courses, tumors were collected from 34 younger women, 17 with good and 17 with poor outcomes, as determined by disease-specific survival during a follow-up period of 17 years. The clinicopathologic parameters of the tumors were complemented with DNA image cytometry profiles, enumeration of copy numbers of eight breast cancer genes by multicolor fluorescence in situ hybridization, and targeted sequence analysis of 563 cancer genes. Both groups included diploid and aneuploid tumors. The degree of intratumor heterogeneity was significantly higher in aneuploid versus diploid cases, and so were gains of the oncogenes MYC and ZNF217. Significantly more copy number alterations were observed in the group with poor outcome. Almost all tumors in the group with long survival were classified as luminal A, whereas triple-negative tumors predominantly occurred in the short survival group. Mutations in PIK3CA were more common in the group with good outcome, whereas TP53 mutations were more frequent in patients with poor outcomes. This study shows that TP53 mutations and the extent of genomic imbalances are associated with poor outcome in younger breast cancer patients and thus emphasize the central role of genomic instability vis-a-vis tumor aggressiveness.
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Affiliation(s)
- Ayla Koçak
- Section for Translational Surgical Oncology and Biobanking, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany; Genetics Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | | | - Annette Lischka
- Section for Translational Surgical Oncology and Biobanking, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Daniela Hirsch
- Genetics Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - David Fiedler
- Genetics Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Yue Hu
- Genetics Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Natalie Doberstein
- Section for Translational Surgical Oncology and Biobanking, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Irianna Torres
- Genetics Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - Wei-Dong Chen
- Genetics Branch, National Cancer Institute, NIH, Bethesda, Maryland
| | - E Michael Gertz
- Computational Biology Branch, National Center for Biotechnology Information, NIH, Bethesda, Maryland; Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, Maryland
| | - Alejandro A Schäffer
- Computational Biology Branch, National Center for Biotechnology Information, NIH, Bethesda, Maryland; Cancer Data Science Laboratory, National Cancer Institute, NIH, Bethesda, Maryland
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, University Hospital Schleswig-Holstein, Kiel, Germany
| | - Jutta Kirfel
- Institute of Pathology, University Hospital Schleswig-Holstein, Lübeck, Germany
| | - Gert Auer
- Department of Oncology-Pathology, Karolinska Biomic Center, Karolinska Institute, Stockholm, Sweden
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck, Germany; Department of Oncology-Pathology, Karolinska Biomic Center, Karolinska Institute, Stockholm, Sweden
| | - Thomas Ried
- Genetics Branch, National Cancer Institute, NIH, Bethesda, Maryland.
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10
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Braun R, Anthuber L, Hirsch D, Wangsa D, Lack J, McNeil NE, Heselmeyer-Haddad K, Torres I, Wangsa D, Brown MA, Tubbs A, Auslander N, Gertz EM, Brauer PR, Cam MC, Sackett DL, Habermann JK, Nussenzweig A, Ruppin E, Zhang Z, Rosenberg DW, Ried T. Single-Cell-Derived Primary Rectal Carcinoma Cell Lines Reflect Intratumor Heterogeneity Associated with Treatment Response. Clin Cancer Res 2020; 26:3468-3480. [PMID: 32253233 DOI: 10.1158/1078-0432.ccr-19-1984] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Revised: 01/22/2020] [Accepted: 04/01/2020] [Indexed: 12/24/2022]
Abstract
PURPOSE The standard treatment of patients with locally advanced rectal cancer consists of preoperative chemoradiotherapy (CRT) followed by surgery. However, the response of individual tumors to CRT is extremely diverse, presenting a clinical dilemma. This broad variability in treatment response is likely attributable to intratumor heterogeneity (ITH). EXPERIMENTAL DESIGN We addressed the impact of ITH on response to CRT by establishing single-cell-derived cell lines (SCDCL) from a treatment-naïve rectal cancer biopsy after xenografting. RESULTS Individual SCDCLs derived from the same tumor responded profoundly different to CRT in vitro. Clonal reconstruction of the tumor and derived cell lines based on whole-exome sequencing revealed nine separate clusters with distinct proportions in the SCDCLs. Missense mutations in SV2A and ZWINT were clonal in the resistant SCDCL, but not detected in the sensitive SCDCL. Single-cell genetic analysis by multiplex FISH revealed the expansion of a clone with a loss of PIK3CA in the resistant SCDCL. Gene expression profiling by tRNA-sequencing identified the activation of the Wnt, Akt, and Hedgehog signaling pathways in the resistant SCDCLs. Wnt pathway activation in the resistant SCDCLs was confirmed using a reporter assay. CONCLUSIONS Our model system of patient-derived SCDCLs provides evidence for the critical role of ITH for treatment response in patients with rectal cancer and shows that distinct genetic aberration profiles are associated with treatment response. We identified specific pathways as the molecular basis of treatment response of individual clones, which could be targeted in resistant subclones of a heterogenous tumor.
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Affiliation(s)
- Rüdiger Braun
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Lena Anthuber
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Daniela Hirsch
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Darawalee Wangsa
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Justin Lack
- NIAID Collaborative Bioinformatics Resource (NCBR), National Institute of Allergy and Infectious Diseases, NIH, Bethesda, Maryland.,Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Nicole E McNeil
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | | | - Irianna Torres
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Danny Wangsa
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Markus A Brown
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Anthony Tubbs
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Noam Auslander
- Cancer Data Science Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - E Michael Gertz
- Cancer Data Science Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Philip R Brauer
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Margaret C Cam
- Office of Science and Technology Resources, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Dan L Sackett
- Eunice Kennedy Shriver National Institute of Child Health & Human Development, NIH, Bethesda, Maryland
| | - Jens K Habermann
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Germany
| | - Andre Nussenzweig
- Laboratory of Genome Integrity, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Eytan Ruppin
- Cancer Data Science Laboratory, Center for Cancer Research, NCI, NIH, Bethesda, Maryland
| | - Zhongqiu Zhang
- Department of Surgery, Waterbury Hospital, University of Connecticut School of Medicine, Waterbury, Connecticut
| | - Daniel W Rosenberg
- Center for Molecular Oncology, University of Connecticut Health, Farmington, Waterbury, Connecticut
| | - Thomas Ried
- Section of Cancer Genomics, Center for Cancer Research, NCI, NIH, Bethesda, Maryland.
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11
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Lermen D, Gwinner F, Bartel-Steinbach M, Mueller SC, Habermann JK, Balwir MB, Smits E, Virgolino A, Fiddicke U, Berglund M, Åkesson A, Bergstrom A, Leander K, Horvat M, Snoj Tratnik J, Posada de la Paz M, Castaño Calvo A, Esteban López M, von Briesen H, Zimmermann H, Kolossa-Gehring M. Towards Harmonized Biobanking for Biomonitoring: A Comparison of Human Biomonitoring-Related and Clinical Biorepositories. Biopreserv Biobank 2020; 18:122-135. [PMID: 32281895 PMCID: PMC7185365 DOI: 10.1089/bio.2019.0092] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Human biomonitoring (HBM) depends on high-quality human samples to identify status and trends in exposure and ensure comparability of results. In this context, much effort has been put into the development of standardized processes and quality assurance for sampling and chemical analysis, while effects of sample storage and shipment on sample quality have been less thoroughly addressed. To characterize the currently applied storage and shipment procedures within the consortium of the European Human Biomonitoring Initiative (HBM4EU), which aims at harmonization of HBM in Europe, a requirement analysis based on data from an online survey was conducted. In addition, the online survey was addressed to professionals in clinical biobanking represented by members of the European, Middle Eastern and African Society for Biopreservation and Biobanking (ESBB) to identify the current state-of-the-art in terms of sample storage and shipment. Results of this survey conducted in these two networks were compared to detect processes with potential for optimization and harmonization. In general, many similarities exist in sample storage and shipment procedures applied by ESBB members and HBM4EU partners and many requirements for ensuring sample quality are already met also by HBM4EU partners. Nevertheless, a need for improvement was identified for individual steps in sample storage, shipment, and related data management with potential impact on sample and data quality for HBM purposes. Based on these findings, recommendations for crucial first steps to further strengthen sample quality, and thus foster advancement in HBM on a pan-European level are given.
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Affiliation(s)
- Dominik Lermen
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- The European Human-Biomonitoring Initiative HBM4EU
| | - Frederik Gwinner
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Martina Bartel-Steinbach
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Sabine C. Mueller
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Jens K. Habermann
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- University Clinical Center Schleswig-Holstein, University of Luebeck, Translational Surgical Oncology and Biobanking, Luebeck, Germany
| | - Matharoo-Ball Balwir
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- Nottingham University Hospital, Translational Research and Nottingham Health Science Biobank (NHSB), Nottingham, United Kingdom
| | - Elke Smits
- European, Middle Eastern & African Society for Biopreservation and Biobanking, Brussels, Belgium
- Antwerp University Hospital, University of Antwerp, Division of Medical Director, Edegem, Belgium
| | - Ana Virgolino
- The European Human-Biomonitoring Initiative HBM4EU
- Faculdade de Medicina, Instituto de Saúde Ambiental, Universidade de Lisboa, Lisboa, Portugal
| | - Ulrike Fiddicke
- The European Human-Biomonitoring Initiative HBM4EU
- German Environment Agency (Umweltbundesamt), Berlin, Germany
| | - Marika Berglund
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Agneta Åkesson
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Anna Bergstrom
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Karin Leander
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Environmental Medicine, Karolinska Institute, Institute of Environmental Medicine (IMM), Stockholm, Sweden
| | - Milena Horvat
- The European Human-Biomonitoring Initiative HBM4EU
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
| | - Janja Snoj Tratnik
- The European Human-Biomonitoring Initiative HBM4EU
- Jožef Stefan Institute, Department of Environmental Sciences, Ljubljana, Slovenia
| | - Manuel Posada de la Paz
- The European Human-Biomonitoring Initiative HBM4EU
- Institute of Rare Diseases Research, CIBERER, EuroBiobanK, Instituto de Salud Carlos III, Madrid, Spain
| | - Argelia Castaño Calvo
- The European Human-Biomonitoring Initiative HBM4EU
- Centro Nacional de Sanidad Ambiental CNSA, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Marta Esteban López
- The European Human-Biomonitoring Initiative HBM4EU
- Centro Nacional de Sanidad Ambiental CNSA, Instituto de Salud Carlos III, Majadahonda, Spain
| | - Hagen von Briesen
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Heiko Zimmermann
- Fraunhofer Institute for Biomedical Engineering IBMT, Biomonitoring & Biobanks, Sulzbach, Germany
- The European Human-Biomonitoring Initiative HBM4EU
| | - Marike Kolossa-Gehring
- The European Human-Biomonitoring Initiative HBM4EU
- German Environment Agency (Umweltbundesamt), Berlin, Germany
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Salchow J, Mann J, Koch B, von Grundherr J, Jensen W, Elmers S, Straub LA, Vettorazzi E, Escherich G, Rutkowski S, Dwinger S, Bergelt C, Sokalska-Duhme M, Bielack S, Calaminus G, Baust K, Classen CF, Rössig C, Faber J, Faller H, Hilgendorf I, Gebauer J, Langer T, Metzler M, Schuster S, Niemeyer C, Puzik A, Reinhardt D, Dirksen U, Sander A, Köhler M, Habermann JK, Bokemeyer C, Stein A. Comprehensive assessments and related interventions to enhance the long-term outcomes of child, adolescent and young adult cancer survivors - presentation of the CARE for CAYA-Program study protocol and associated literature review. BMC Cancer 2020; 20:16. [PMID: 31906955 PMCID: PMC6945396 DOI: 10.1186/s12885-019-6492-5] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [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: 03/25/2019] [Accepted: 12/23/2019] [Indexed: 12/21/2022] Open
Abstract
Background Improved, multimodal treatment strategies have been shown to increase cure rates in cancer patients. Those who survive cancer as a child, adolescent or young adult (CAYA), are at a higher risk for therapy-, or disease-related, late or long-term effects. The CARE for CAYA-Program has been developed to comprehensively assess any potential future problems, to offer need-based preventative interventions and thus to improve long-term outcomes in this particularly vulnerable population. Methods The trial is designed as an adaptive trial with an annual comprehensive assessment followed by needs stratified, modular interventions, currently including physical activity, nutrition and psycho-oncology, all aimed at improving the lifestyle and/or the psychosocial situation of the patients. Patients, aged 15–39 years old, with a prior cancer diagnosis, who have completed tumour therapy and are in follow-up care, and who are tumour free, will be included. At baseline (and subsequently on an annual basis) the current medical and psychosocial situation and lifestyle of the participants will be assessed using a survey compiled of various validated questionnaires (e.g. EORTC QLQ C30, NCCN distress thermometer, PHQ-4, BSA, nutrition protocol) and objective parameters (e.g. BMI, WHR, co-morbidities like hyperlipidaemia, hypertension, diabetes), followed by basic care (psychological and lifestyle consultation). Depending on their needs, CAYAs will be allocated to preventative interventions in the above-mentioned modules over a 12-month period. After 1 year, the assessment will be repeated, and further interventions may be applied as needed. During the initial trial phase, the efficacy of this approach will be compared to standard care (waiting list with intervention in the following year) in a randomized study. During this phase, 530 CAYAs will be included and 320 eligible CAYAs who are willing to participate in the interventions will be randomly allocated to an intervention. Overall, 1500 CAYAs will be included and assessed. The programme is financed by the innovation fund of the German Federal Joint Committee and will be conducted at 14 German sites. Recruitment began in January 2018. Discussion CAYAs are at high risk for long-term sequelae. Providing structured interventions to improve lifestyle and psychological situation may counteract against these risk factors. The programme serves to establish uniform regular comprehensive assessments and need-based interventions to improve long-term outcome in CAYA survivors. Trial registration Registered at the German Clinical Trial Register (ID: DRKS00012504, registration date: 19th January 2018).
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Affiliation(s)
- J Salchow
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany.
| | - J Mann
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - B Koch
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - J von Grundherr
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - W Jensen
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - S Elmers
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - L A Straub
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - E Vettorazzi
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - G Escherich
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - S Rutkowski
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - S Dwinger
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - C Bergelt
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - S Bielack
- Klinikum Stuttgart, Olgahospital, Stuttgart, Germany
| | | | - K Baust
- University Hospital Bonn, Bonn, Germany
| | - C F Classen
- University Hospital Rostock, Rostock, Germany
| | - C Rössig
- University Children's Hospital Münster, Münster, Germany
| | - J Faber
- Mainz University Medical Center, Mainz, Germany
| | - H Faller
- University Hospital Würzburg, Würzburg, Germany
| | | | - J Gebauer
- University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - T Langer
- University Hospital of Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - M Metzler
- University Hospital Erlangen, Erlangen, Germany
| | - S Schuster
- University Hospital Erlangen, Erlangen, Germany
| | - C Niemeyer
- Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - A Puzik
- Medical Centre, Faculty of Medicine, University of Freiburg, Freiburg, Germany
| | - D Reinhardt
- University Hospital Essen, Essen, Germany.,German Cancer Consortium, Essen, Germany
| | - U Dirksen
- University Hospital Essen, Essen, Germany.,German Cancer Consortium, Essen, Germany
| | - A Sander
- Hannover Medical School, Hannover, Germany
| | - M Köhler
- Medical Faculty University Hospital Magdeburg, Magdeburg, Germany
| | | | - C Bokemeyer
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - A Stein
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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13
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Kock-Schoppenhauer AK, Kroll B, Lambarki M, Ulrich H, Stahl-Toyota S, Habermann JK, Duhm-Harbeck P, Ingenerf J, Lablans M. One Step Away from Technology but One Step Towards Domain Experts-MDRBridge: A Template-Based ISO 11179-Compliant Metadata Processing Pipeline. Methods Inf Med 2019; 58:e72-e79. [PMID: 31853911 DOI: 10.1055/s-0039-3399579] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
BACKGROUND Secondary use of routine medical data relies on a shared understanding of given information. This understanding is achieved through metadata and their interconnections, which can be stored in metadata repositories (MDRs). The necessity of an MDR is well understood, but the local work on metadata is a time-consuming and challenging process for domain experts. OBJECTIVE To support the identification, collection, and provision of metadata in a predefined structured manner to foster consolidation. A particular focus is placed on user acceptance. METHODS We propose a software pipeline MDRBridge as a practical intermediary for metadata capture and processing, based on MDRSheet, an ISO 11179-3 compliant template using popular spreadsheet software. It serves as a practical mediator for metadata acquisition and processing in a broader pipeline. Due to the different origins of the metadata, both manual entry and automatic extractions from application systems are supported. To enable the export of collected metadata into external MDRs, a mapping of ISO 11179 to Clinical Data Interchange Standards Consortium (CDISC) Operational Data Model (ODM) was developed. RESULTS MDRSheet is embedded in the processing pipeline MDRBridge and delivers metadata in the CDISC ODM format for further use in MDRs. This approach is used to interactively unify core datasets, import existing standard datasets, and automatically extract all defined data elements from source systems. The involvement of clinical domain experts improved significantly due to minimal changes within their usual work routine. CONCLUSION A high degree of acceptance was achieved by adapting the working methods of clinical domain experts. The designed process is capable of transforming all relevant data elements according to the ISO 11179-3 format. MDRSheet is used as an intermediate format to present the information at a glance and to allow editing or supplementing by domain experts.
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Affiliation(s)
| | - B Kroll
- IT Center for Clinical Research, University of Lübeck, Germany
| | - M Lambarki
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
| | - H Ulrich
- IT Center for Clinical Research, University of Lübeck, Germany
| | - S Stahl-Toyota
- Medical Informatics for Translational Oncology, German Cancer Research Center, Heidelberg, Germany
| | - J K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck & University Clinical Center Schleswig-Holstein, Campus Lübeck, Germany.,Interdisciplinary Center for Biobanking-Lübeck (ICB-L), University of Lübeck, Germany
| | - P Duhm-Harbeck
- IT Center for Clinical Research, University of Lübeck, Germany
| | - J Ingenerf
- Institute of Medical Informatics, University of Lübeck, Germany
| | - M Lablans
- Federated Information Systems, German Cancer Research Center, Heidelberg, Germany
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14
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Hüneburg R, Aretz S, Büttner R, Daum S, Engel C, Fechner G, Habermann JK, Heling D, Hoffmann K, Holinski-Feder E, Kloor M, von Knebel-Döberitz M, Loeffler M, Möslein G, Perne C, Redler S, Rieß O, Schmiegel W, Seufferlein T, Siebers-Renelt U, Steinke-Lange V, Tecklenburg J, Vangala D, Vilz T, Weitz J, Wiedenmann B, Strassburg CP, Nattermann J. [Current recommendations for surveillance, risk reduction and therapy in Lynch syndrome patients]. Z Gastroenterol 2019; 57:1309-1320. [PMID: 31739377 DOI: 10.1055/a-1008-9827] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
INTRODUCTION Lynch syndrome (LS) is the most common hereditary colorectal cancer syndrome and accounts for ~3 % of all CRCs. This autosomal dominant disorder is caused by germline mutations in DNA mismatch repair genes (MLH1, MSH2, MSH6, PMS2, and EPCAM). One in 300 individuals of the general population are considered to be mutation carriers (300 000 individuals/Germany). Mutation carriers are at a high CRC risk of 15-46 % till the age of 75 years. LS also includes a variety of extracolonic malignancies such as endometrial, small bowel, gastric, urothelial, and other cancers. METHODS The German Consortium for Familial Intestinal Cancer consists of 14 university centers in Germany. The aim of the consortium is to develop and evaluate surveillance programs and to further translate the results in clinical care. We have revisited and updated the clinical management guidelines for LS patients in Germany. RESULTS A surveillance colonoscopy should be performed every 12-24 months starting at the age of 25 years. At diagnosis of first colorectal cancer, an oncological resection is advised, an extended resection (colectomy with ileorectal anastomosis) has to be discussed with the patient. The lifetime risk for gastric cancer is 0.2-13 %. Gastric cancers detected during surveillance have a lower tumor stage compared to symptom-driven detection. The lifetime risk for small bowel cancer is 4-8 %. About half of small bowel cancer is located in the duodenum and occurs before the age of 35 years in 10 % of all cases. Accordingly, patients are advised to undergo an esophagogastroduodenoscopy every 12-36 months starting by the age of 25 years. CONCLUSION LS colonic and extracolonic clinical management, surveillance and therapy are complex and several aspects remain unclear. In the future, surveillance and clinical management need to be more tailored to gene and gender. Future prospective trials are needed.
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Affiliation(s)
- Robert Hüneburg
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Bonn.,Nationales Zentrum für erbliche Tumorerkrankungen, Universitätsklinikum Bonn
| | - Stefan Aretz
- Nationales Zentrum für erbliche Tumorerkrankungen, Universitätsklinikum Bonn.,Institut für Humangenetik, Universitätsklinikum Bonn
| | | | - Severin Daum
- Medizinische Klinik für Gastroenterologie, Infektiologie und Rheumatologie, Charité Berlin
| | - Christoph Engel
- Institut für Medizinische Informatik, Statistik und Epidemiologie (IMISE), Universität Leipzig
| | - Guido Fechner
- Nationales Zentrum für erbliche Tumorerkrankungen, Universitätsklinikum Bonn.,Klinik und Poliklinik für Urologie, Universitätsklinikum Bonn
| | - Jens K Habermann
- Sektion für Translationale Chirurgische Onkologie & Biomaterialien, Klinik für Chirurgie und Institut für Humangenetik, Universität zu Lübeck und Universitätsklinikum Schleswig-Holstein, Campus Lübeck
| | - Dominik Heling
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Bonn.,Nationales Zentrum für erbliche Tumorerkrankungen, Universitätsklinikum Bonn
| | - Katrin Hoffmann
- Institut für Humangenetik, Martin-Luther-Universität Halle-Wittenberg
| | - Elke Holinski-Feder
- Medizinisch-Genetisches Zentrum (MGZ) München.,Klinikum der Universität München Campus Innenstadt, Medizinische Klinik und Poliklinik IV, München
| | - Matthias Kloor
- Institut für angewandte Tumorbiologie, Universitätsklinikum Heidelberg
| | | | - Markus Loeffler
- Institut für Medizinische Informatik, Statistik und Epidemiologie (IMISE), Universität Leipzig
| | - Gabriela Möslein
- Zentrum für hereditäre Tumorerkrankungen, Helios-Universitätsklinik Wuppertal, Universität Witten-Herdecke
| | - Claudia Perne
- Nationales Zentrum für erbliche Tumorerkrankungen, Universitätsklinikum Bonn.,Institut für Humangenetik, Universitätsklinikum Bonn
| | - Silke Redler
- Institut für Humangenetik, Universitätsklinikum Düsseldorf
| | - Olaf Rieß
- Institut für Medizinische Genetik und angewandte Genomik, Universitätsklinikum Tübingen
| | - Wolff Schmiegel
- Medizinische Klinik, Universitätsklinikum Knappschaftskrankenhaus Bochum
| | | | | | - Verena Steinke-Lange
- Medizinisch-Genetisches Zentrum (MGZ) München.,Klinikum der Universität München Campus Innenstadt, Medizinische Klinik und Poliklinik IV, München
| | | | - Deepak Vangala
- Medizinische Klinik, Universitätsklinikum Knappschaftskrankenhaus Bochum
| | - Tim Vilz
- Nationales Zentrum für erbliche Tumorerkrankungen, Universitätsklinikum Bonn.,Klinik und Poliklinik für Allgemein-, Viszeral-, Thorax- und Gefäßchirurgie, Universitätsklinikum Bonn
| | - Jürgen Weitz
- Klinik und Poliklinik für Viszeral-, Thorax- und Gefäßchirurgie, Universitätsklinikum Dresden
| | - Bertram Wiedenmann
- Medizinische Klinik m. S. Hepatologie und Gastroenterologie, Charité Berlin
| | - Christian P Strassburg
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Bonn.,Nationales Zentrum für erbliche Tumorerkrankungen, Universitätsklinikum Bonn
| | - Jacob Nattermann
- Medizinische Klinik und Poliklinik I, Universitätsklinikum Bonn.,Nationales Zentrum für erbliche Tumorerkrankungen, Universitätsklinikum Bonn
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15
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Flügge F, Figge L, Duhm-Harbeck P, Kammler R, Habermann JK. How clinical biobanks can support precision medicine: from standardized preprocessing to treatment guidance. Expert Review of Precision Medicine and Drug Development 2019. [DOI: 10.1080/23808993.2019.1690395] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Affiliation(s)
- Friedemann Flügge
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
| | - Lena Figge
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
| | | | - Rosita Kammler
- Translational Research Coordination for International Breast Cancer Study Group and European Thoracic Oncology Platform, Bern, Switzerland
- European, Middle Eastern and African Society for Biopreservation and Biobanking, Brussels, Belgium
| | - Jens K. Habermann
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Lübeck, Germany
- European, Middle Eastern and African Society for Biopreservation and Biobanking, Brussels, Belgium
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein (UKSH), Lübeck, Germany
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16
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Gemoll T, Miroll E, Klein O, Lischka A, Eravci M, Thorns C, Habermann JK. Spatial UBE2N protein expression indicates genomic instability in colorectal cancers. BMC Cancer 2019; 19:710. [PMID: 31319803 PMCID: PMC6639966 DOI: 10.1186/s12885-019-5856-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 11/08/2018] [Accepted: 06/19/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND One major hallmark of colorectal cancers (CRC) is genomic instability with its contribution to tumor heterogeneity and therapy resistance. To facilitate the investigation of intra-sample phenotypes and the de novo identification of tumor sub-populations, imaging mass spectrometry (IMS) provides a powerful technique to elucidate the spatial distribution patterns of peptides and proteins in tissue sections. METHODS In the present study, we analyzed an in-house compiled tissue microarray (n = 60) comprising CRCs and control tissues by IMS. After obtaining protein profiles through direct analysis of tissue sections, two validation sets were used for immunohistochemical evaluation. RESULTS A total of 28 m/z values in the mass range 800-3500 Da distinguished euploid from aneuploid CRCs (p < 0.001, ROC AUC values < 0.385 or > 0.635). After liquid chromatograph-mass spectrometry identification, UBE2N could be successfully validated by immunohistochemistry in the initial sample cohort (p = 0.0274, ROC AUC = 0.7937) and in an independent sample set of 90 clinical specimens (p = 0.0070, ROC AUC = 0.6957). CONCLUSIONS The results showed that FFPE protein expression profiling of surgically resected CRC tissue extracts by MALDI-TOF MS has potential value for improved molecular classification. Particularly, the protein expression of UBE2N was validated in an independent clinical cohort to distinguish euploid from aneuploid CRCs.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.
| | - Elena Miroll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Oliver Klein
- Berlin-Brandenburg Center for Regenerative Therapies, Charité - Universitätsmedizin Berlin, Berlin, Germany
| | - Annette Lischka
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Murat Eravci
- Institute of Chemistry and Biochemistry, Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Christoph Thorns
- Institute of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany.,Interdisciplinary Center for Biobanking-Lübeck (ICB-L), University of Lübeck, Lübeck, Germany
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17
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Braun R, Ronquist S, Wangsa D, Chen H, Anthuber L, Gemoll T, Wangsa D, Koparde V, Hunn C, Habermann JK, Heselmeyer-Haddad K, Rajapakse I, Ried T. Single Chromosome Aneuploidy Induces Genome-Wide Perturbation of Nuclear Organization and Gene Expression. Neoplasia 2019; 21:401-412. [PMID: 30909073 PMCID: PMC6434407 DOI: 10.1016/j.neo.2019.02.003] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2019] [Revised: 02/22/2019] [Accepted: 02/26/2019] [Indexed: 12/21/2022] Open
Abstract
Chromosomal aneuploidy is a defining feature of carcinomas and results in tumor-entity specific genomic imbalances. For instance, most sporadic colorectal carcinomas carry extra copies of chromosome 7, an aneuploidy that emerges already in premalignant adenomas, and is maintained throughout tumor progression and in derived cell lines. A comprehensive understanding on how chromosomal aneuploidy affects nuclear organization and gene expression, i.e., the nucleome, remains elusive. We now analyzed a cell line established from healthy colon mucosa with a normal karyotype (46,XY) and its isogenic derived cell line that acquired an extra copy of chromosome 7 as its sole anomaly (47,XY,+7). We studied structure/function relationships consequent to aneuploidization using genome-wide chromosome conformation capture (Hi-C), RNA sequencing and protein profiling. The gain of chromosome 7 resulted in an increase of transcript levels of resident genes as well as genome-wide gene and protein expression changes. The Hi-C analysis showed that the extra copy of chromosome 7 is reflected in more interchromosomal contacts between the triploid chromosomes. Chromatin organization changes are observed genome-wide, as determined by changes in A/B compartmentalization and topologically associating domain (TAD) boundaries. Most notably, chromosome 4 shows a profound loss of chromatin organization, and chromosome 14 contains a large A/B compartment switch region, concurrent with resident gene expression changes. No changes to the nuclear position of the additional chromosome 7 territory were observed when measuring distances of chromosome painting probes by interphase FISH. Genome and protein data showed enrichment in signaling pathways crucial for malignant transformation, such as the HGF/MET-axis. We conclude that a specific chromosomal aneuploidy has profound impact on nuclear structure and function, both locally and genome-wide. Our study provides a benchmark for the analysis of cancer nucleomes with complex karyotypes.
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Affiliation(s)
- Rüdiger Braun
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Scott Ronquist
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Darawalee Wangsa
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Haiming Chen
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA
| | - Lena Anthuber
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Danny Wangsa
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Vishal Koparde
- CCR Collaborative Bioinformatics Resource (CCBR), Center for Cancer Research, NCI, Bethesda, MD, USA; Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research sponsored by the National Cancer Institute, Frederick, MD, USA
| | - Cynthia Hunn
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Kerstin Heselmeyer-Haddad
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA
| | - Indika Rajapakse
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI, USA; Department of Mathematics, University of Michigan, Ann Arbor, MI, USA.
| | - Thomas Ried
- Section of Cancer Genomics, National Cancer Institute, Center for Cancer Research, NIH, Bethesda, MD, USA.
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18
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Oltmann J, Heselmeyer-Haddad K, Hernandez LS, Meyer R, Torres I, Hu Y, Doberstein N, Killian JK, Petersen D, Zhu YJ, Edelman DC, Meltzer PS, Schwartz R, Gertz EM, Schäffer AA, Auer G, Habermann JK, Ried T. Aneuploidy, TP53 mutation, and amplification of MYC correlate with increased intratumor heterogeneity and poor prognosis of breast cancer patients. Genes Chromosomes Cancer 2018; 57:165-175. [PMID: 29181861 PMCID: PMC5807164 DOI: 10.1002/gcc.22515] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [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: 10/02/2017] [Revised: 11/21/2017] [Accepted: 11/24/2017] [Indexed: 01/01/2023] Open
Abstract
The clinical course of breast cancer varies from one patient to another. Currently, the choice of therapy relies on clinical parameters and histological and molecular tumor features. Alas, these markers are informative in only a subset of patients. Therefore, additional predictors of disease outcome would be valuable for treatment stratification. Extensive studies showed that the degree of variation of the nuclear DNA content, i.e., aneuploidy, determines prognosis. Our aim was to further elucidate the molecular basis of aneuploidy. We analyzed five diploid and six aneuploid tumors with more than 20 years of follow-up. By performing FISH with a multiplexed panel of 10 probes to enumerate copy numbers in individual cells, and by sequencing 563 cancer-related genes, we analyzed how aneuploidy is linked to intratumor heterogeneity. In our cohort, none of the patients with diploid tumors died of breast cancer during follow-up in contrast to four of six patients with aneuploid tumors (mean survival 86.4 months). The FISH analysis showed markedly increased genomic instability and intratumor heterogeneity in aneuploid tumors. MYC gain was observed in only 20% of the diploid cancers, while all aneuploid cases showed a gain. The mutation burden was similar in diploid and aneuploid tumors, however, TP53 mutations were not observed in diploid tumors, but in all aneuploid tumors in our collective. We conclude that quantitative measurements of intratumor heterogeneity by multiplex FISH, detection of MYC amplification and TP53 mutation could augment prognostication in breast cancer patients.
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Affiliation(s)
- Johanna Oltmann
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck, Lübeck, Germany
| | - Kerstin Heselmeyer-Haddad
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Leanora S. Hernandez
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Rüdiger Meyer
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Irianna Torres
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Yue Hu
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Natalie Doberstein
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck, Lübeck, Germany
| | - J. Keith Killian
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - David Petersen
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Y. Jack Zhu
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Daniel C. Edelman
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Paul S. Meltzer
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
| | - Russell Schwartz
- Department of Biological Sciences and Computational Biology Department, Carnegie Mellon University, Pittsburgh, PA
| | - E. Michael Gertz
- Computational Biology Branch, National Center for Biotechnology Information/National Institutes of Health, Bethesda, MD, USA
| | - Alejandro A. Schäffer
- Computational Biology Branch, National Center for Biotechnology Information/National Institutes of Health, Bethesda, MD, USA
| | - Gert Auer
- Department of Pathology and Oncology, Karolinska University Hospital and Karolinska Institute, Stockholm, Sweden
| | - Jens K. Habermann
- Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck, Lübeck, Germany
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute/National Institutes of Health, Bethesda, MD
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19
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ElSharawy A, Röder C, Becker T, Habermann JK, Schreiber S, Rosenstiel P, Kalthoff H. Concentration of circulating miRNA-containing particles in serum enhances miRNA detection and reflects CRC tissue-related deregulations. Oncotarget 2018; 7:75353-75365. [PMID: 27683108 PMCID: PMC5342746 DOI: 10.18632/oncotarget.12205] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [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: 02/08/2016] [Accepted: 09/12/2016] [Indexed: 01/02/2023] Open
Abstract
The emerging potential of miRNAs as biomarkers for cancer detection demands parallel evaluation of strategies for reliable identification of disease-related signatures from easily accessible and pertinent body compartments. Here, we addressed whether efficient concentration of circulating miRNA-carrying particles is a rationale for miRNA biomarker discovery. We systematically compared miRNA signatures in 93 RNA preparations from three serum entities (whole serum, particle-concentrated, and particle-depleted fractions) and corresponding tissue samples from patients with colorectal cancer (CRC) as a model disease. Significant differences between whole sera and particle-concentrated serum fractions of CRC patients emerged for 45 of 742 tested miRNAs. Twenty-eight of these 45 miRNAs were differentially expressed between particle-concentrated serum fractions of metastatic CRC- and healthy individuals. Over half of these candidates (15 of 28) showed deregulations only in concentrated serum fractions, but not in whole sera, compared to the respective controls.Our results also provided evidence of a consistent downregulation of miR-486 and miR-92a, and further showed a possible "strand-specific" deregulation of extracellular miRNAs in CRC. More importantly, most of the identified miRNAs in the enriched sera reflected the patterns of the corresponding tumor tissues and showed links to cancer-related inflammation. Further investigation of seven serum pools revealed a subset of potential extracellular miRNA candidates to be implicated in both neoplastic and inflammatory bowel disease.Our findings demonstrate that enrichment and sensitive detection of miRNA carriers is a promising approach to detect CRC-related pathological changes in liquid biopsies, and has potential for clinical diagnostics.
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Affiliation(s)
- Abdou ElSharawy
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.,Faculty of Sciences, Division of Biochemistry, Department of Chemistry, Damietta University, New Damietta City, Egypt
| | - Christian Röder
- Institute for Experimental Cancer Research, Christian-Albrechts-University, Kiel, Germany
| | - Thomas Becker
- Department of General Surgery, Visceral, Thoracic, Transplantation and Pediatric Surgery, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Stefan Schreiber
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany.,Clinic for Internal Medicine I, University Hospital Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Philip Rosenstiel
- Institute of Clinical Molecular Biology, Christian-Albrechts-University, Kiel, Germany
| | - Holger Kalthoff
- Institute for Experimental Cancer Research, Christian-Albrechts-University, Kiel, Germany
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20
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Acun T, Doberstein N, Habermann JK, Gemoll T, Thorns C, Oztas E, Ried T. HLJ1 (DNAJB4) Gene Is a Novel Biomarker Candidate in Breast Cancer. OMICS 2018; 21:257-265. [PMID: 28481734 DOI: 10.1089/omi.2017.0016] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
Breast cancer is the most common cancer type and cause of cancer-related mortality among women worldwide. New biomarker discovery is crucial for diagnostic innovation and personalized medicine in breast cancer. Heat shock proteins (HSPs) have been increasingly reported as biomarkers and potential drug targets for cancers. HLJ1 (DNAJB4) belongs to the DNAJ (HSP40) family of HSPs and is regarded as a tumor suppressor gene in lung, colon, and gastric cancers. However, the role of the HLJ1 gene in breast cancer is currently unknown. We evaluated the role of the HLJ1 gene in breast cancer progression by analyzing its in vitro and in vivo expression and its genetic/epigenetic alterations. HLJ1 expression was found to be reduced or lost in breast cancer cell lines (SK-BR-3, MDA-MB-231, ZR-75-1) compared with the nontumorigenic mammary epithelial cell line (MCF 10A). In a clinical context for breast cancer progression, the HLJ1 expression was significantly less frequent in invasive breast carcinoma samples (n = 230) compared with normal breast tissue (n = 100), benign neoplasia (n = 53), and ductal carcinoma in situ (n = 21). In methylation analyses by the combined bisulfite restriction analysis assay, the CpG island located in the 5'-flanking region of the HLJ1 gene was found to be methylated in breast cancer cell lines. HLJ1 expression was restored in the ZR-75-1 cell line by DNA demethylating agent 5-Aza-2'-deoxycytidine (5-AzadC) and histone deacetylase inhibitor trichostatin A. These new observations support the idea that HLJ1 is a tumor suppressor candidate and potential biomarker for breast cancer. Epigenomic mechanisms such as CpG methylation and histone deacetylation might contribute to downregulation of HLJ1 expression. We call for future functional, epigenomic, and clinical studies to ascertain the contribution of HLJ1 to breast cancer pathogenesis and, importantly, evaluate its potential for biomarker development in support of personalized medicine diagnostic innovation in clinical oncology.
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Affiliation(s)
- Tolga Acun
- 1 Department of Molecular Biology and Genetics, Bülent Ecevit University , Zonguldak, Turkey
| | - Natalie Doberstein
- 2 Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein , Lübeck, Germany
| | - Jens K Habermann
- 2 Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein , Lübeck, Germany
| | - Timo Gemoll
- 2 Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein , Lübeck, Germany
| | - Christoph Thorns
- 3 Institute of Pathology, University of Lübeck and University Medical Center Schleswig-Holstein , Lübeck, Germany
| | - Emin Oztas
- 4 Department of Medical Histology and Embryology, Gülhane Military Medical Academy , Ankara, Turkey
| | - Thomas Ried
- 5 Genetics Branch, Center for Cancer Research, National Cancer Institute, National Institutes of Health , Bethesda, Maryland
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21
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Strohkamp S, Gemoll T, Humborg S, Hartwig S, Lehr S, Freitag-Wolf S, Becker S, Franzén B, Pries R, Wollenberg B, Roblick UJ, Bruch HP, Keck T, Auer G, Habermann JK. Protein levels of clusterin and glutathione synthetase in platelets allow for early detection of colorectal cancer. Cell Mol Life Sci 2017; 75:323-334. [PMID: 28849249 DOI: 10.1007/s00018-017-2631-9] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [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: 03/27/2017] [Revised: 07/21/2017] [Accepted: 08/21/2017] [Indexed: 02/06/2023]
Abstract
Colorectal cancer (CRC) is one of the most frequent malignancies in the Western world. Early tumor detection and intervention are important determinants on CRC patient survival. During early tumor proliferation, dissemination and angiogenesis, platelets store and segregate proteins actively and selectively. Hence, the platelet proteome is a potential source of biomarkers denoting early malignancy. By comparing protein profiles of platelets between healthy volunteers (n = 12) and patients with early- (n = 7) and late-stage (n = 5) CRCs using multiplex fluorescence two-dimensional gel electrophoresis (2D-DIGE), we aimed at identifying differentially regulated proteins within platelets. By inter-group comparisons, 94 differentially expressed protein spots were detected (p < 0.05) between healthy controls and patients with early- and late-stage CRCs and revealed distinct separations between all three groups in principal component analyses. 54 proteins of interest were identified by mass spectrometry and resulted in high-ranked Ingenuity Pathway Analysis networks associated with Cellular function and maintenance, Cellular assembly and organization, Developmental disorder and Organismal injury and abnormalities (p < 0.0001 to p = 0.0495). Target proteins were validated by multiplex fluorescence-based Western blot analyses using an additional, independent cohort of platelet protein samples [healthy controls (n = 15), early-stage CRCs (n = 15), late-stage CRCs (n = 15)]. Two proteins-clusterin and glutathione synthetase (GSH-S)-featured high impact and were subsequently validated in this independent clinical cohort distinguishing healthy controls from patients with early- and late-stage CRCs. Thus, the potential of clusterin and GSH-S as platelet biomarkers for early detection of CRC could improve existing screening modalities in clinical application and should be confirmed in a prospective multicenter trial.
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Affiliation(s)
- Sarah Strohkamp
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
| | - Sina Humborg
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Sonja Hartwig
- Institute of Clinical Biochemistry and Pathobiochemistry, Leibniz Center for Diabetes Research, German Diabetes Center at the Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Stefan Lehr
- Institute of Clinical Biochemistry and Pathobiochemistry, Leibniz Center for Diabetes Research, German Diabetes Center at the Heinrich-Heine-University Düsseldorf, Düsseldorf, Germany.,German Center for Diabetes Research (DZD), München-Neuherberg, Germany
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, University Medical Center Schleswig-Holstein, Campus Kiel, Kiel, Germany
| | - Susanne Becker
- Karolinska Biomics Center, Karolinska Institutet, Stockholm, Sweden
| | - Bo Franzén
- Karolinska Biomics Center, Karolinska Institutet, Stockholm, Sweden
| | - Ralph Pries
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Barbara Wollenberg
- Clinic for Otorhinolaryngology, Head and Neck Surgery, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Uwe J Roblick
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Hans-Peter Bruch
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Tobias Keck
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Gert Auer
- Karolinska Biomics Center, Karolinska Institutet, Stockholm, Sweden
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany. .,Interdisciplinary Center for Biobanking-Lübeck (ICB-L), University of Lübeck, Lübeck, Germany.
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22
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Hoellen F, Waldmann A, Banz-Jansen C, Holtrich U, Karn T, Oberländer M, Habermann JK, Hörmann M, Köster F, Ribbat-Idel J, Thill M, Rody A, El-Balat A, Hanker L. Claudin-1 expression in cervical cancer. Mol Clin Oncol 2017; 7:880-884. [PMID: 29181184 DOI: 10.3892/mco.2017.1391] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [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: 03/10/2017] [Accepted: 08/17/2017] [Indexed: 11/06/2022] Open
Abstract
Claudin-1 is a tight junction protein that has been demonstrated to be involved in tumorigenesis and tumor progression in various types of solid tumors. In the present study, the protein expression of claudin-1 in squamous cervical cancer tissues obtained from 106 patients was analyzed by immunohistochemistry. In addition, the grade of claudin-1 expression was analyzed for associations with certain clinicopathological parameters. A significant overexpression of claudin-1 was detected in the tumor cells, when compared with that in the peritumoral stroma. There was no significant association between claudin-1 expression and FIGO stage, tumor size, grading or the appearance of distant metastases. Cervical cancer patients scoring positive for claudin-1 protein expression tended to exhibit more lymph node metastasis (28.3%), compared with claudin-1-negative patients (7.1%). Regarding overall survival, the results of the present study suggest a better prognosis for claudin-1-negative patients. In order to elucidate whether claudin-1 overexpression has a significant prognostic impact on squamous cervical cancer, further studies are required.
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Affiliation(s)
- Friederike Hoellen
- Department of Gynecology and Obstetrics, University of Lübeck, D-23538 Lübeck, Germany
| | - Annika Waldmann
- Institute for Social Medicine and Epidemiology, University of Lübeck, D-23538 Lübeck, Germany
| | - Constanze Banz-Jansen
- Department of Gynecology and Obstetrics, University Hospital Oldenburg, D-26133 Oldenburg, Germany
| | - Uwe Holtrich
- Department of Obstetrics and Gynecology, Goethe-University, D-60590 Frankfurt, Germany
| | - Thomas Karn
- Department of Obstetrics and Gynecology, Goethe-University, D-60590 Frankfurt, Germany
| | - Martina Oberländer
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany.,Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany.,Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Mareike Hörmann
- Institute for Pathology, University of Düsseldorf, D-40225 Düsseldorf, Germany
| | - Frank Köster
- Department of Gynecology and Obstetrics, University of Lübeck, D-23538 Lübeck, Germany
| | | | - Marc Thill
- Department of Gynecology and Obstetrics, Agaplesion Markus Krankenhaus, D-60431 Frankfurt, Germany
| | - Achim Rody
- Department of Gynecology and Obstetrics, University of Lübeck, D-23538 Lübeck, Germany
| | - Ahmed El-Balat
- Department of Obstetrics and Gynecology, Goethe-University, D-60590 Frankfurt, Germany
| | - Lars Hanker
- Department of Gynecology and Obstetrics, University of Lübeck, D-23538 Lübeck, Germany
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23
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Epp A, Hobusch J, Bartsch YC, Petry J, Lilienthal GM, Koeleman CAM, Eschweiler S, Möbs C, Hall A, Morris SC, Braumann D, Engellenner C, Bitterling J, Rahmöller J, Leliavski A, Thurmann R, Collin M, Moremen KW, Strait RT, Blanchard V, Petersen A, Gemoll T, Habermann JK, Petersen F, Nandy A, Kahlert H, Hertl M, Wuhrer M, Pfützner W, Jappe U, Finkelman FD, Ehlers M. Sialylation of IgG antibodies inhibits IgG-mediated allergic reactions. J Allergy Clin Immunol 2017; 141:399-402.e8. [PMID: 28728998 DOI: 10.1016/j.jaci.2017.06.021] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2016] [Revised: 05/31/2017] [Accepted: 06/14/2017] [Indexed: 01/09/2023]
Affiliation(s)
- Alexandra Epp
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Juliane Hobusch
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Yannic C Bartsch
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Janina Petry
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Gina-Maria Lilienthal
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Carolien A M Koeleman
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Simon Eschweiler
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Christian Möbs
- Department of Dermatology and Allergology, Philipps University Marburg, Marburg, Germany
| | - Ashley Hall
- Division of Emergency Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Suzanne C Morris
- Division of Immunology, Allergy and Rheumatology, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Dominique Braumann
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany; Laboratory of Glycodesign and Glycoanalytics, Institute for Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-University Medicine Berlin, Berlin, Germany
| | - Christine Engellenner
- Division of Biochemical Immunology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Josephine Bitterling
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Johann Rahmöller
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany; Department of Anesthesiology and Intensive Care, University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Alexei Leliavski
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Robina Thurmann
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany
| | - Mattias Collin
- Division of Infection Medicine, Department of Clinical Sciences, Lund University, Lund, Sweden
| | - Kelley W Moremen
- Complex Carbohydrate Research Center, University of Georgia, Athens, Ga
| | - Richard T Strait
- Division of Emergency Medicine, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Pediatrics, University of Cincinnati College of Medicine, Cincinnati, Ohio
| | - Véronique Blanchard
- Laboratory of Glycodesign and Glycoanalytics, Institute for Laboratory Medicine, Clinical Chemistry and Pathobiochemistry, Charité-University Medicine Berlin, Berlin, Germany
| | - Arnd Petersen
- Division of Clinical & Molecular Allergology, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany
| | - Timo Gemoll
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University of Lübeck & Univesity Medical Center Schleswig Holstein, Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology & Biobanking, Department of Surgery, University of Lübeck & Univesity Medical Center Schleswig Holstein, Lübeck, Germany
| | - Frank Petersen
- Division of Biochemical Immunology, Research Center Borstel, Leibniz-Center for Medicine and Biosciences, Borstel, Germany
| | - Andreas Nandy
- Research and Preclinical Development, Allergopharma GmbH & Co. KG, a business of Merck, Darmstadt, Germany
| | - Helga Kahlert
- Research and Preclinical Development, Allergopharma GmbH & Co. KG, a business of Merck, Darmstadt, Germany
| | - Michael Hertl
- Department of Dermatology and Allergology, Philipps University Marburg, Marburg, Germany
| | - Manfred Wuhrer
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Leiden, The Netherlands
| | - Wolfgang Pfützner
- Department of Dermatology and Allergology, Philipps University Marburg, Marburg, Germany
| | - Uta Jappe
- Division of Clinical & Molecular Allergology, Research Center Borstel, Airway Research Center North (ARCN), German Center for Lung Research (DZL), Borstel, Germany; Interdisciplinary Allergy Outpatient Clinic, Department of Internal Medicine, University of Lübeck, Lübeck, Germany
| | - Fred D Finkelman
- Division of Immunology, Allergy and Rheumatology, Department of Medicine, University of Cincinnati College of Medicine, Cincinnati, Ohio; Division of Immunobiology, Cincinnati Children's Hospital Medical Center, Cincinnati, Ohio; Department of Medicine, Cincinnati Veterans Affairs Medical Center, Cincinnati, Ohio
| | - Marc Ehlers
- Laboratories of Immunology and Antibody Glycan Analysis, Institute for Nutrition Medicine, University of Lübeck & University Medical Center Schleswig Holstein, Lübeck, Germany.
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24
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Gemoll T, Kollbeck SL, Karstens KF, Hò GG, Hartwig S, Strohkamp S, Schillo K, Thorns C, Oberländer M, Kalies K, Lehr S, Habermann JK. EB1 protein alteration characterizes sporadic but not ulcerative colitis associated colorectal cancer. Oncotarget 2017; 8:54939-54950. [PMID: 28903393 PMCID: PMC5589632 DOI: 10.18632/oncotarget.18978] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [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: 02/14/2017] [Accepted: 06/17/2017] [Indexed: 12/29/2022] Open
Abstract
Background While carcinogenesis in Sporadic Colorectal Cancer (SCC) has been thoroughly studied, less is known about Ulcerative Colitis associated Colorectal Cancer (UCC). This study aimed to identify and validate differentially expressed proteins between clinical samples of SCC and UCC to elucidate new insights of UCC/SCC carcinogenesis and progression. Results Multiplex-fluorescence two-dimensional gel electrophoresis (2-D DIGE) and mass spectrometry identified 67 proteoforms representing 43 distinct proteins. After analysis by Ingenuity Pathway Analysis® (IPA), subsequent Western blot validation proofed the differential expression of Heat shock 27 kDA protein 1 (HSPB1) and Microtubule-associated protein R/EB family, member 1 (EB1) while the latter one showed also expression differences by immunohistochemistry. Materials and Methods Fresh frozen tissue of UCC (n = 10) matched with SCC (n = 10) was investigated. Proteins of cancerous intestinal mucosal cells were obtained by Laser Capture Microdissection (LCM) and compared by 2-D DIGE. Significant spots were identified by mass spectrometry. After IPA, three proteins [EB1, HSPB1, and Annexin 5 (ANXA5)] were chosen for further validation by Western blotting and tissue microarray-based immunohistochemistry. Conclusions This study identified significant differences in protein expression of colorectal carcinoma cells from UCC patients compared to patients with SCC. Particularly, EB1 was validated in an independent clinical cohort.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Sophie L Kollbeck
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Karl F Karstens
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Gia G Hò
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Sonja Hartwig
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Düsseldorf, Leibniz Center for Diabetes Research, D-40225 Düsseldorf, Germany.,German Center for Diabetes Research (DZD), D-85764 München-Neuherberg, Germany
| | - Sarah Strohkamp
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Katharina Schillo
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Christoph Thorns
- Department of Pathology, University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Martina Oberländer
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
| | - Kathrin Kalies
- Institute of Anatomy, University of Lübeck, D-23538 Lübeck, Germany
| | - Stefan Lehr
- Institute of Clinical Biochemistry and Pathobiochemistry, German Diabetes Center at the Heinrich-Heine-University Düsseldorf, Leibniz Center for Diabetes Research, D-40225 Düsseldorf, Germany.,German Center for Diabetes Research (DZD), D-85764 München-Neuherberg, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Hospital Schleswig-Holstein, Campus Lübeck, D-23538 Lübeck, Germany
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25
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Meyer R, Freitag-Wolf S, Blindow S, Büning J, Habermann JK. Combining aneuploidy and dysplasia for colitis' cancer risk assessment outperforms current surveillance efficiency: a meta-analysis. Int J Colorectal Dis 2017; 32:171-182. [PMID: 27766414 DOI: 10.1007/s00384-016-2684-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Accepted: 10/11/2016] [Indexed: 02/04/2023]
Abstract
PURPOSE Cancer risk assessment for ulcerative colitis patients by evaluating histological changes through colonoscopy surveillance is still challenging. Thus, additional parameters of high prognostic impact for the development of colitis-associated carcinoma are necessary. This meta-analysis was conducted to clarify the value of aneuploidy as predictor for individual cancer risk compared with current surveillance parameters. METHODS A systematic web-based search identified studies published in English that addressed the relevance of the ploidy status for individual cancer risk during surveillance in comparison to neoplastic mucosal changes. The resulting data were included into a meta-analysis, and odds ratios (OR) were calculated for aneuploidy or dysplasia or aneuploidy plus dysplasia. RESULTS Twelve studies addressing the relevance of aneuploidy compared to dyplasia were comprehensively evaluated and further used for meta-analysis. The meta-analysis revealed that aneuploidy (OR 5.31 [95 % CI 2.03, 13.93]) is an equally effective parameter for cancer risk assessment in ulcerative colitis patients as dysplasia (OR 4.93 [1.61, 15.11]). Strikingly, the combined assessment of dysplasia and aneuploidy is superior compared to applying each parameter alone (OR 8.99 [3.08, 26.26]). CONCLUSIONS This meta-analysis reveals that aneuploidy is an equally effective parameter for individual cancer risk assessment in ulcerative colitis as the detection of dysplasia. More important, the combined assessment of dysplasia and aneuploidy outperforms the use of each parameter alone. We suggest image cytometry for ploidy assessment to become an additional feature of consensus criteria to individually assess cancer risk in UC.
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Affiliation(s)
- Rüdiger Meyer
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.,Section of Cancer Genomics, Genetics Branch, National Cancer Institute, National Institutes of Health, 50 South Drive, Bethesda, MD, 20892, USA
| | - Sandra Freitag-Wolf
- Institute of Medical Informatics and Statistics, University Medical Center Schleswig-Holstein, Campus Kiel, Brunswiker Straße 10, 24105, Kiel, Germany
| | - Silke Blindow
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Jürgen Büning
- Unit of Gastroenterology, Department of Internal Medicine I, University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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Hoellen F, Waldmann A, Banz-Jansen C, Rody A, Heide M, Köster F, Ribbat-Idel J, Thorns C, Gebhard M, Oberländer M, Habermann JK, Thill M. Expression of cyclooxygenase-2 in cervical cancer correlates with lymphangiosis carcinomatosa. Geburtshilfe Frauenheilkd 2016. [DOI: 10.1055/s-0036-1592727] [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] Open
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Gemoll T, Strohkamp S, Schillo K, Thorns C, Habermann JK. MALDI-imaging reveals thymosin beta-4 as an independent prognostic marker for colorectal cancer. Oncotarget 2016; 6:43869-80. [PMID: 26556858 PMCID: PMC4791273 DOI: 10.18632/oncotarget.6103] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [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: 06/16/2015] [Accepted: 10/11/2015] [Indexed: 12/13/2022] Open
Abstract
DNA aneuploidy has been identified as a prognostic factor for epithelial malignancies. Matrix-assisted laser desorption/ionization (MALDI) imaging mass spectrometry (IMS) is a powerful tool for direct analysis of multiple proteins in tissue sections while maintaining the cellular and molecular integrity. We compared diploid and aneuploid colon cancer tissues against normal mucosa of the colon by means of IMS. DNA image cytometry determined the ploidy status of tissue samples that were subsequently subjected to MALDI-IMS. After obtaining protein profiles through direct analysis of tissue sections, a discovery and independent validation set were used to predict ploidy status by applying proteomic classification algorithms [Supervised Neural Network (SNN) and Receiver Operating Characteristic (ROC)]. Five peaks (m/z 2,395 and 4,977 for diploid vs. aneuploid comparison as well as m/z 3,376, 6,663, and 8,581 for normal mucosa vs. carcinoma comparison) were significant in both SNN and ROC analysis. Among these, m/z 4,977 was identified as thymosin beta 4 (Tβ-4). Tβ-4 was subsequently validated in clinical samples using a tissue microarray to predict overall survival in colon cancer patients.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Sarah Strohkamp
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Katharina Schillo
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Christoph Thorns
- Department of Pathology, University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Lübeck, Germany
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Ahmad-Nejad P, Duda A, Sucker A, Werner M, Bronsert P, Stickeler E, Reifenberger G, Malzkorn B, Oberländer M, Habermann JK, Bruch HP, Linnebacher M, Schadendorf D, Neumaier M. Assessing quality and functionality of DNA isolated from FFPE tissues through external quality assessment in tissue banks. Clin Chem Lab Med 2016; 53:1927-34. [PMID: 26053008 DOI: 10.1515/cclm-2014-1202] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2014] [Accepted: 04/30/2015] [Indexed: 11/15/2022]
Abstract
BACKGROUND Biobanks are becoming increasingly important for assessment of disease risk as well as identification and validation of new diagnostic biomarkers and druggable targets. The validity of data obtained from biobanks is critically limited by the biomaterial quality of the biological samples. External quality assessment (EQA) programs suitable to comprehensively measure the biomaterial quality in archived materials are currently lacking. We report on quantitative assay designs for the analysis of both structural and functional integrity of DNAs that were applied in a first pilot EQA within the priority program on tumor tissue biobanking funded by the German Cancer Aid. METHODS Participating biobanks isolated DNAs from a standardized set of 10 samples comprising sections of four different formalin-fixed paraffin-embedded tissues using their standard operating procedures. Isolated DNAs and analytical results were returned and analyzed centrally for nucleic acids yield, purity, fragmentation and amplificability at a quantitative level using dedicated assay designs. RESULTS The amount of extracted DNA varied in isolates ranging between 1.5 μg and 25.8 μg. Quantification of DNA fragmentation and amplificability allowed to highlight considerable discrepancies in DNA quality. Amplicons yielded from the isolates of these identical EQA samples ranged from 105 to 411 bp suggesting differences between residual inhibitors of downstream enzymatic reactions. CONCLUSIONS The quality of extraction of bioanalytes from biomaterial archives is heterogeneous even for stable biomolecules like DNA isolated with highly standardized methods. EQAs are appropriate tools to uncover strengths and weaknesses in biobanks in a systematic fashion. Biomaterial integrity is insufficiently reflected by standard methods, but needs to be assessed to improve biobank interoperability. Finally, our results also point towards the problem of measuring the quality of more delicate biomolecules like proteins or metabolites.
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Hoellen F, Waldmann A, Banz-Jansen C, Rody A, Heide M, Köster F, Ribbat-Idel J, Thorns C, Gebhard M, Oberländer M, Habermann JK, Thill M. Expression of cyclooxygenase-2 in cervical cancer is associated with lymphovascular invasion. Oncol Lett 2016; 12:2351-2356. [PMID: 27698799 PMCID: PMC5038214 DOI: 10.3892/ol.2016.4925] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [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: 01/22/2016] [Accepted: 05/23/2016] [Indexed: 12/14/2022] Open
Abstract
Cyclooxygenase-2 (COX-2) is associated with carcinogenesis and tumor progression. The current study analyzed the effect of COX-2 expression in patients with invasive squamous cervical cancer. Tissue samples from 123 cervical cancer patients were collected for a retrospective analysis using immunohistochemistry (IHC) with an antibody against COX-2. The clinical and survival data of the patients were analyzed. Positive staining for COX-2 (defined as an immunoreactivity score of ≥4) was detected in 28 patients (23%), with significantly higher percentages of staining in tumor cells compared with peritumoral stroma cells (P<0.001). COX-2 expression was significantly associated with lymphovascular space invasion (LVSI; P=0.017). The association of COX-2 expression with LVSI suggests a possible effect of COX-2 on tumor progression in cervical cancer. Further studies including larger patient collectives are required in order to perform analyses of clinical subgroups and patient survival.
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Affiliation(s)
- Friederike Hoellen
- Department of Gynecology and Obstetrics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck Campus, Lübeck D-23538, Germany
| | - Annika Waldmann
- Institute for Social Medicine and Epidemiology, University of Lübeck, Lübeck D-23538, Germany
| | - Constanze Banz-Jansen
- Department of Gynecology and Obstetrics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck Campus, Lübeck D-23538, Germany
| | - Achim Rody
- Department of Gynecology and Obstetrics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck Campus, Lübeck D-23538, Germany
| | - Maria Heide
- Department of Gynecology and Obstetrics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck Campus, Lübeck D-23538, Germany
| | - Frank Köster
- Department of Gynecology and Obstetrics, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck Campus, Lübeck D-23538, Germany
| | | | - Christoph Thorns
- Institute for Pathology, University of Lübeck, Lübeck D-23538, Germany
| | | | - Martina Oberländer
- Department of Surgery, Section for Translational Surgical Oncology and Biobanking, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck Campus, Lübeck D-23562, Germany
| | - Jens K Habermann
- Department of Surgery, Section for Translational Surgical Oncology and Biobanking, University of Lübeck and University Hospital Schleswig-Holstein, Lübeck Campus, Lübeck D-23562, Germany
| | - Marc Thill
- Department of Gynecology and Obstetrics, Agaplesion Markus Hospital, Frankfurt D-60431, Germany
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Bünger S, Zimmermann M, Habermann JK. Diversity of assessing circulating tumor cells (CTCs) emphasizes need for standardization: a CTC Guide to design and report trials. Cancer Metastasis Rev 2016; 34:527-45. [PMID: 26323491 DOI: 10.1007/s10555-015-9582-0] [Citation(s) in RCA: 19] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Abstract
Hematogenous spreading of tumor cells from primary tumors is a crucial step in the cascade to metastasis, the latter being the most limiting factor for patients' survival prognosis. Therefore, circulating tumor cells (CTCs) have become a field of intensive research. However, the process of isolation and identification of CTCs lacks standardization. This article presents an overview of 71 CTC studies reported in PUBMED since 2000 and focusing on colorectal cancer. These studies are evaluated regarding standardization of CTC isolation and identification, marker proteins used, study population and blood sample quality management, clinical performance, and quality measures. Overall, standardization of CTC assessment seems insufficient. Thus, comparability of CTC studies is hampered and results should be interpreted carefully. We here propose a standardized CTC guideline (CTC Guide) to prospectively design and report studies/trials in a harmonized form. Despite the current interstudy heterogeneity, the data indicate that CTC detection is of clinical relevance and CTCs should be considered as a surrogate prognostic marker. Many studies indicate the high potential for CTCs as prognostic markers, e.g., in colorectal cancer treatment. However, standardized, large-scale multicenter validation studies are still needed to pave the way for clinical implementation of CTC detection that could ameliorate individualized medicine regimes.
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Affiliation(s)
- S Bünger
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - M Zimmermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany
| | - J K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Ratzeburger Allee 160, 23538, Lübeck, Germany.
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Meyer R, McNeil NE, Krawczyk E, Rosenberg DW, Zhang Z, Schlegel R, Habermann JK, Ried T. Abstract 2402: The impact of genomic heterogeneity in colorectal carcinoma on therapy response - a study on monoclonal primary colon cultures. Cancer Res 2016. [DOI: 10.1158/1538-7445.am2016-2402] [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: 11/16/2022]
Abstract
Abstract
Introduction: Individual response to chemotherapy in colorectal cancer patients is highly variable and the underlying mechanisms of treatment resistance of colorectal cancer cells are poorly understood. Recent studies revealed a considerable degree of genomic and genetic tumor heterogeneity. We hypothesize that the intra-tumoral heterogeneity has a direct impact on treatment response as sub-populations of cancer cells are resistant to currently used chemotherapeutics and facilitate tumor growth under treatment.
Experimental procedures: Patient-derived primary colorectal cell lines were established employing three different methodological approaches: (i) mouse xenografts and reintroduction of the graft to culture, (ii) conditional reprogramming by Rho kinase inhibition in combination with irradiated feeder cells and (iii) organoid growth in Matrigel with Wnt-, R-spondin and Noggin conditioned medium. Established primary cultures were characterized genomically by array CGH and spectral karyotyping (SKY).
Results: To date, we successfully established eight patient-derived primary colorectal cell lines. Culture conditions were optimized for long-term in vitro growth of colorectal primary tissue. Array CGH has identified patterns of chromosomal imbalances in these cell lines, i.e. gains of chromosomes 7, 13 and 20 as well as a loss of chromosome 18. Additionally, gene amplifications of MYC and EGFR were identified. As these aberrations are typically found in colorectal cancer, the established primary tissue derived cell lines closely reflect the nature of the tumor in vivo in terms of genomic instability. Array CGH findings were confirmed using SKY. Sub-cultivation of single cell derived monoclonal cell lines will facilitate addressing the tumor heterogeneity in terms of their genomic and genetic background using genome and transcriptome analyses. Single-cell derived lines will then be exposed to chemotherapeutic drugs currently used in clinical routine such as 5-FU and Oxaliplatin. The respective sensitivity will be correlated to the aberration profiles.
Conclusion: Exploration of tumor heterogeneity in terms of their genomic and genetic background in the context of treatment response might facilitate understanding of therapy resistance. Moreover, reliable prediction of the patient's response to the employed chemotherapeutic drug is a necessary step towards individualized treatment in colorectal cancer.
Citation Format: Rüdiger Meyer, Nicole E. McNeil, Ewa Krawczyk, Daniel W. Rosenberg, Zhongqiu Zhang, Richard Schlegel, Jens K. Habermann, Thomas Ried. The impact of genomic heterogeneity in colorectal carcinoma on therapy response - a study on monoclonal primary colon cultures. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 2402.
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Affiliation(s)
- Rüdiger Meyer
- 1Section of Cancer Genomics, Genetics Branch, NCI, National Institutes of Health, Bethesda, MD
| | - Nicole E. McNeil
- 1Section of Cancer Genomics, Genetics Branch, NCI, National Institutes of Health, Bethesda, MD
| | - Ewa Krawczyk
- 2Center for Cell Reprogramming,Georgetown University Medical Center, Washington, DC
| | - Daniel W. Rosenberg
- 3Center for Molecular Medicine, University of Connecticut Health Center, Farmington, CT
| | - Zhongqiu Zhang
- 4Department of Surgery, Waterbury Hospital, University of Connecticut School of Medicine, Waterbury, CT
| | - Richard Schlegel
- 2Center for Cell Reprogramming,Georgetown University Medical Center, Washington, DC
| | - Jens K. Habermann
- 5Section of Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck, Lübeck, Germany
| | - Thomas Ried
- 1Section of Cancer Genomics, Genetics Branch, NCI, National Institutes of Health, Bethesda, MD
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Lange T, Valentiner U, Wicklein D, Maar H, Labitzky V, Brauns AK, Streichert T, Otto B, Sauter G, Wolters-Eisfeld G, Riecken K, Bà ¶rnchen C, Kiefmann R, Abraham V, DeLisser HM, Gemoll T, Habermann JK, Schumacher U. E-selectin ligand binding affinity to determine anti-metastatic efficacy of proteasome inhibition. J Clin Oncol 2016. [DOI: 10.1200/jco.2016.34.15_suppl.e23010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Affiliation(s)
- Tobias Lange
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | - Daniel Wicklein
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Hanna Maar
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Vera Labitzky
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Benjamin Otto
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | - Guido Sauter
- Hubertus Wald Cancer Center, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | | | - Rainer Kiefmann
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
| | | | | | - Timo Gemoll
- University Medical Center Schleswig-Holstein, Lubeck, Germany
| | | | - Udo Schumacher
- University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Ulrich H, Kock AK, Duhm-Harbeck P, Habermann JK, Ingenerf J. Metadata Repository for Improved Data Sharing and Reuse Based on HL7 FHIR. Stud Health Technol Inform 2016; 228:162-166. [PMID: 27577363] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Unreconciled data structures and formats are a common obstacle to the urgently required sharing and reuse of data within healthcare and medical research. Within the North German Tumor Bank of Colorectal Cancer, clinical and sample data, based on a harmonized data set, is collected and can be pooled by using a hospital-integrated Research Data Management System supporting biobank and study management. Adding further partners who are not using the core data set requires manual adaptations and mapping of data elements. Facing this manual intervention and focusing the reuse of heterogeneous healthcare instance data (value level) and data elements (metadata level), a metadata repository has been developed. The metadata repository is an ISO 11179-3 conformant server application built for annotating and mediating data elements. The implemented architecture includes the translation of metadata information about data elements into the FHIR standard using the FHIR Data Element resource with the ISO 11179 Data Element Extensions. The FHIR-based processing allows exchange of data elements with clinical and research IT systems as well as with other metadata systems. With increasingly annotated and harmonized data elements, data quality and integration can be improved for successfully enabling data analytics and decision support.
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Affiliation(s)
- Hannes Ulrich
- Institute of Medical Informatics, University of Lübeck, Germany
| | | | | | - Jens K Habermann
- Interdisciplinary Center for Biobanking-Lübeck, University of Lübeck, Germany
| | - Josef Ingenerf
- Institute of Medical Informatics, University of Lübeck, Germany
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Gemoll T, Meyer R, Habermann JK. Applying Genomics and Proteomics in Translational Surgical Oncology Research. Eur Surg Res 2015; 55:184-97. [PMID: 26339997 DOI: 10.1159/000438860] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2015] [Accepted: 07/20/2015] [Indexed: 11/19/2022]
Abstract
BACKGROUND Translational surgical research can range from investigating clinically oriented basic pathophysiological research via the correlation of molecular findings with a patient's clinical outcome to conducting treatment response studies. Herein, the specialist's opinion as a 'surgeon scientist' plays a pivotal role, e.g. in planning experimental setups focusing on the clinically most relevant needs. SUMMARY AND KEY MESSAGES: This review provides a survey of genomic and proteomic technologies and gives an up-to-date overview of those studies applying these technologies exemplarily in colorectal cancer-based biomarker research. Although current results are promising, future validation studies within multicenter networks are required to promote the translation of 'omics' from bench to bedside. In this endeavor, departments of surgery and institutes of experimental surgery together should play a fundamental role. The program for 'clinician scientists' recently launched by the German Research Society (DFG) could be one tool to promote interdisciplinary networks and surgeons' impact on translational research.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lx00FC;beck and University Medical Center Schleswig-Holstein (UKSH), Lx00FC;beck, Germany
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Gerling M, Meyer KF, Fuchs K, Igl BW, Fritzsche B, Ziegler A, Bader F, Kujath P, Schimmelpenning H, Bruch HP, Roblick UJ, Habermann JK. High Frequency of Aneuploidy Defines Ulcerative Colitis-Associated Carcinomas: A Prognostic Comparison to Sporadic Colorectal Carcinomas. Ann Surg 2015; 252:74-83. [PMID: 20531006 DOI: 10.1097/sla.0b013e3181deb664] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
OBJECTIVE Aneuploidy is an independent risk factor for forthcoming carcinogenesis in ulcerative colitis (UC). An inferior prognosis of patients with ulcerative colitis-associated colorectal cancer (UCC) compared with those with sporadic colorectal cancer (SCC) has been reported, but remains controversial. This prompted us to investigate if aneuploidy can be observed in UCCs as frequently as in their sporadic counterpart and if aneuploidy per se might be a driving feature of poor prognosis in UCC. BACKGROUND DATA We obtained clinical follow-up for 257 SCC patients (average observation time 57 months) and 31 UCC patients (51 months). Touch preparation slides or tissue sections were prepared of all 288 carcinomas for ploidy analysis. METHODS Ploidy status was assessed for 260 SCCs and 31 UCCs by image cytometry and correlated to clinical features. Survival data were analyzed using Kaplan-Meier estimates. RESULTS Aneuploidy was detected in 74.6% of SCCs and in all 31 UCCs. Logistic regression analysis yielded age (odds ratio [OR], 1.05; 95% CI, 1.02-1.09; P = 0.003) and aneuploidy (OR, 4.07; 95% CI, 1.46-11.36; P = 0.007) as independent prognostic factors for R0-resected patients devoid of metastases. Diploid SCCs had a more favorable 5-year survival (88.2%) than aneuploid SCCs (69.0%) and UCCs (73.1%) (P = 0.074). CONCLUSIONS UC-associated carcinomas presented aneuploidy at significantly higher frequency than sporadic colorectal carcinomas (P < 0.0006). UCCs and aneuploid SCCs share a similar prognosis inferior to that of diploid SCCs. Aneuploidy proved to be the strongest independent prognostic marker for R0-resected colorectal cancer patients overall.
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Affiliation(s)
- Marco Gerling
- Laboratory for Surgical Research, Department of Surgery, University Clinic Schleswig-Holstein, Lübeck, Germany
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Abstract
Genetic instability is a striking feature of human cancers, with an impact on the genesis, progression and prognosis. The clinical importance of genomic instability and aneuploidy is underscored by its association with poor patient outcome in multiple cancer types, including breast and colon cancer. Interestingly, there is growing evidence that prognostic gene expression signatures simply reflect the degree of genomic instability. Additionally, also the proteome is affected by aneuploidy and has therefore become a powerful tool to screen for new targets for therapy, diagnosis and prognostication. In this context, the chapter presents the impact of genomic instability on disease prognostication occurring in human cancers.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck & University Medical Center Schleswig-Holstein, Lübeck, Germany
| | - Gert Auer
- Karolinska Biomic Center, Karolinska Institutet, Stockholm, Sweden
| | - Thomas Ried
- Genetics Branch, Center for Cancer Research, National Cancer Institute, NIH, Bethesda, USA
| | - Jens K Habermann
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck & University Medical Center Schleswig-Holstein, Lübeck, Germany.
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Thorns C, Schurmann C, Gebauer N, Wallaschofski H, Kümpers C, Bernard V, Feller AC, Keck T, Habermann JK, Begum N, Lehnert H, Brabant G. Global microRNA profiling of pancreatic neuroendocrine neoplasias. Anticancer Res 2014; 34:2249-2254. [PMID: 24778027] [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] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
BACKGROUND Pancreatic neuroendocrine neoplasms (pNEN) are rare tumors with a poor prognosis. Although increasing data have accumulated on the molecular pathology of pNEN, very scarce data exist on microRNAs in pNEN and no data are published on microRNAs as potential biomarkers of pNEN in serum. This study aimed to identify microRNA signatures of pNEN in tissue and serum. MATERIALS AND METHODS We included tissue samples from 37 patients with pNEN, 9 patients with non-neoplastic pancreatic pathology, seven samples of micro-dissected pancreatic islets and serum samples of 27 patients with pNEN, as well as of 15 healthy volunteers. MicroRNA expression profiles were established using real-time quantitative Polymerase Chain reaction (PCR) for 754 microRNAs. RESULTS MicroRNA signatures differed between pNEN, pancreatic islets and total pancreas, with virtually no overlap between the groups of de-regulated microRNAs. Expression of miR-642 correlated with Ki67 (MiB1) score and miR-210 correlated with metastatic disease. When comparing microRNA levels in serum from patients with pNEN and healthy volunteers, 13 microRNAs were more abundant in the serum of patients. MiR-193b was also up-regulated in pNEN tissue when compared to pancreatic islets and remained significantly increased in serum even when corrected for multiple testing. CONCLUSION Evaluation of microRNAs appears to be promising in the assessment of pNEN. In particular, miR-193b, which is also increased in serum, may be a potential new biomarker of pNEN.
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Affiliation(s)
- Chistoph Thorns
- Institut für Pathologie, Universität zu Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany.
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Bünger S, Klempt-Giessing K, Toner V, Kelly M, FitzGerald SP, Brenner H, von Eggeling F, Habermann JK. A novel multiplex-protein array for serum diagnostics of colorectal cancer: impact of pre-analytical storage conditions. Biopreserv Biobank 2013; 11:379-86. [PMID: 24835368 DOI: 10.1089/bio.2013.0050] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [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] Open
Abstract
INTRODUCTION Biomarker discovery studies seldom report on pre-analytical effects. We used a novel multiplex protein biochip for colorectal cancer screening to investigate effects of different storage temperatures and repeated freeze-thaw cycles. METHODS This biochip, composed of CEA, IL-8, VEGF, M-CSF, S100A11, C3adesArg, CD26, and CRP, was applied to twenty highly standardized preserved serum samples. RESULTS Aliquot comparison of long-term storage at -80°C (n=20) versus -170°C (n=20) did not show significant differences for any of the eight markers. In contrast, three freeze-thaw cycles (3 × 20 aliquots) detected changes in the serum level for all markers (p<0.05) but S100A11 and CD26: levels of CEA, IL-8, C3adesArg, and CRP increased, while VEGF and M-CSF levels decreased. However, applying diagnostic thresholds for CEA, IL-8, and CRP revealed that freeze-thaw cycles did not affect diagnostic performance. In contrast, analysis of samples stored at -80°C compared to -170°C failed to detect one out of three detectable malignancies. CONCLUSION We conclude that three freeze-thaw cycles modulated serum marker levels significantly, but do not compromise biochip diagnostic performance. For our marker panel, serum preservation at -80°C seems comparable to -170°C; however, storage at -80°C could lead to misdiagnosis. Our findings emphasize the need for standardized sample collection, processing, storage, and reporting.
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Affiliation(s)
- Stefanie Bünger
- 1 Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck , Lübeck, Germany
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Lin YN, Izbicki JR, König A, Habermann JK, Blechner C, Lange T, Schumacher U, Windhorst S. Expression of DIAPH1 is up-regulated in colorectal cancer and its down-regulation strongly reduces the metastatic capacity of colon carcinoma cells. Int J Cancer 2013; 134:1571-82. [PMID: 24105619 DOI: 10.1002/ijc.28486] [Citation(s) in RCA: 26] [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: 04/11/2013] [Accepted: 08/27/2013] [Indexed: 12/25/2022]
Abstract
In most cases, metastatic colorectal cancer is not curable, thus new approaches are necessary to identify novel targets for colorectal cancer therapy. Actin-binding-proteins (ABPs) directly regulate motility of metastasising tumor cells, and for cortactin an association with colon cancer metastasis has been already shown. However, as its depletion only incompletely inhibits metastasis, additional, more suitable cellular targets have to be identified. Here we analyzed expression of the ABPs, DIAPH1, VASP, N-WASP, and fascin in comparison with cortactin and found that, besides cortactin, DIAPH1 was expressed with the highest frequency (63%) in colorectal cancer. As well as cortactin, DIAPH1 was not detectable in normal colon tissue and expression of both proteins was positively correlated with metastasis of colorectal cancer. To analyse the mechanistic role of DIAPH1 for metastasis of colon carcinoma cells in comparison with cortactin, expression of the proteins was stably down-regulated in the human colon carcinoma cell lines HT-29, HROC-24 and HCT-116. Analysis of metastasis of colon carcinoma cells in SCID mice revealed that depletion of DIAPH1 reduced metastasis 60-fold and depletion of cortactin 16-fold as compared with control cells. Most likely the stronger effect of DIAPH1 depletion on colon cancer metastasis is due to the fact that in vitro knock down of DIAPH1 impaired all steps of metastasis; adhesion, invasion and migration while down-regulation of cortactin only reduced adhesion and invasion. This very strong reducing effect of DIAPH1 depletion on colon carcinoma cell metastasis makes the protein a promising therapeutic target for individualized colorectal cancer therapy.
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Affiliation(s)
- Yuan-Na Lin
- Department of General Visceral and Thoracic Surgery, University Medical Center Hamburg-Eppendorf, Hamburg, Germany; Department of Biochemistry and Signal Transduction, University Medical Center Hamburg-Eppendorf, Hamburg, Germany
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Gemoll T, Löwe O, Borén M, Oberländer M, Hartwig S, Lehr S, Roblick UJ, Auer G, Jörnvall H, Habermann JK. The impact of pre-analytical conditions on the serum proteome: heat-stabilization versus nitrogen storage. Arch Physiol Biochem 2013; 119:100-7. [PMID: 23826811 DOI: 10.3109/13813455.2013.806556] [Citation(s) in RCA: 4] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
CONTEXT Biological material reflecting the in vivo composition of markers provides a high potential for biomarker discovery. OBJECTIVE We compared the serum proteome following heat- and nitrogen-preservation, with and without subsequent storage at room temperature. MATERIALS AND METHODS Serum samples were collected, treated and analysed by two-dimensional gel electrophoresis. Protein spots were identified and confirmed by two mass spectrometry approaches (MALDI & ESI) and subjected to Ingenuity Pathway Analysis. RESULTS We revealed 24 differentially expressed proteins (p ≤ 0.05) between nitrogen and heat preservation, and 87 between nitrogen and heat preservation with subsequent storage for 120 h at room-temperature. Mass spectrometry identified 25 polypeptides. Pathway analysis resulted in networks maintaining Cellular Assembly and Organization, Movement and Maintenance. CONCLUSION Heat-stabilization does not substantially change the short-term proteome composition of serum compared with nitrogen treatment. However, heat-stabilization alone seems insufficient for long-term sample preservation for serum samples. We identified transthyretin and apolipoprotein A-IV as sample quality markers.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology and Biobanking, Department of Surgery, University of Lübeck and University Medical Center Schleswig-Holstein, Campus Lübeck, Germany.
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Oberländer M, Linnebacher M, König A, Bogoevska V, Brodersen C, Kaatz R, Krohn M, Hackmann M, Ingenerf J, Christoph J, Mate S, Prokosch HU, Yekebas EF, Thorns C, Büning J, Prall F, Uhlig R, Roblick UJ, Izbicki JR, Klar E, Bruch HP, Vollmar B, Habermann JK. The "North German Tumor Bank of Colorectal Cancer": status report after the first 2 years of support by the German Cancer Aid Foundation. Langenbecks Arch Surg 2013; 398:251-8. [PMID: 23292500 DOI: 10.1007/s00423-012-1043-4] [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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2012] [Accepted: 12/14/2012] [Indexed: 01/08/2023]
Abstract
PURPOSE Research projects and clinical trials strongly rely on high-quality biospecimens which are provided by biobanks. Since differences in sample processing and storage can strongly affect the outcome of such studies, standardization between biobanks is necessary to guarantee reliable results of large, multicenter studies. The German Cancer Aid Foundation (Deutsche Krebshilfe e.V.) has therefore initiated the priority program "tumor tissue banks" in 2010 by funding four biobank networks focusing on central nervous system tumors, melanomas, breast carcinomas, and colorectal carcinomas. The latter one, the North German Tumor Bank of Colorectal Cancer (ColoNet) is managed by surgeons, pathologists, gastroenterologists, oncologists, scientists, and medical computer scientists. METHODS AND RESULTS The ColoNet consortium has developed and harmonized standard operating procedures concerning all biobanking aspects. Crucial steps for quality assurance have been implemented and resulted in certification according to DIN EN ISO 9001. A further achievement is the construction of a web-based database for exploring available samples. In addition, common scientific projects have been initiated. Thus, ColoNet's repository will be used for research projects in order to improve early diagnosis, therapy, follow-up, and prognosis of colorectal cancer patients. Apart from the routine sample storage at -170 °C, the tumor banks' unique characteristic is the participation of outpatient clinics and private practices to further expand the sample and clinical data collection. CONCLUSION The first 2 years of funding by the German Cancer Aid Foundation have already led to a closer scientific connection between the participating institutions and to a substantial collection of biospecimens obtained under highly standardized conditions.
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Zentis PD, Frohnapfel M, Rantanen V, Weidtkamp-Peters S, Felekyan S, Kühnemuth R, Sisamakis E, Xu L, Perols A, Arden-Jacob J, Zilles A, Oberländer M, Fritzsche B, Nygren PÅ, Eriksson Karlström A, Hautaniemi S, Drexhage KH, Auer G, Habermann JK, Widengren J, Seidel CA. Cancer Diagnostics by Multiparameter Fluorescence Image Spectroscopy: A Bioinformatic Classifier Trained on Cultured Immunostained Cells. Biophys J 2013. [DOI: 10.1016/j.bpj.2012.11.1900] [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: 10/27/2022] Open
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Gemoll T, Habermann JK, Becker S, Szymczak S, Upender MB, Bruch HP, Hellman U, Ried T, Auer G, Jörnvall H, Roblick UJ. Chromosomal aneuploidy affects the global proteome equilibrium of colorectal cancer cells. Anal Cell Pathol (Amst) 2013; 36:149-61. [PMID: 24464829 PMCID: PMC4605604 DOI: 10.3233/acp-140088] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/24/2023] Open
Abstract
BACKGROUND Chromosomal aneuploidy has been identified as a prognostic factor in the majority of sporadic carcinomas. However, it is not known how chromosomal aneuploidy affects chromosome-specific protein expression in particular, and the cellular proteome equilibrium in general. OBJECTIVE The aim was to detect chromosomal aneuploidy-associated expression changes in cell clones carrying trisomies found in colorectal cancer. METHODS We used microcell-mediated chromosomal transfer to generate three artificial trisomic cell clones of the karyotypically stable, diploid, yet mismatch-deficient, colorectal cancer cell line DLD1--each of them harboring one extra copy of either chromosome 3, 7 or 13. Protein expression differences were assessed by two-dimensional gel electrophoresis and mass spectrometry, compared to whole-genome gene expression data, and evaluated by PANTHER classification system and Ingenuity Pathway Analysis (IPA). RESULTS In total, 79 differentially expressed proteins were identified between the trisomic clones and the parental cell line. Up-regulation of PCNA and HMGB1 as well as down-regulation of IDH3A and PSMB3 were revealed as trisomy-associated alterations involved in regulating genome stability. CONCLUSIONS These results show that trisomies affect the expression of genes and proteins that are not necessarily located on the trisomic chromosome, but reflect a pathway-related alteration of the cellular equilibrium.
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Affiliation(s)
- Timo Gemoll
- Section for Translational Surgical Oncology & BiobankingDepartment of SurgeryUniversity of LübeckLübeckGermany
- Karolinska Biomic CenterKarolinska InstitutetStockholmSweden
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- *Timo Gemoll:
| | - Jens K. Habermann
- Section for Translational Surgical Oncology & BiobankingDepartment of SurgeryUniversity of LübeckLübeckGermany
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
- Center for Cancer ResearchNational Cancer InstituteNIHBethesdaMDUSA
- *Jens K. Habermann:
| | - Susanne Becker
- Karolinska Biomic CenterKarolinska InstitutetStockholmSweden
| | - Silke Szymczak
- Institute of Medical Biometry and StatisticsUniversity of LübeckLübeckGermany
| | | | - Hans-Peter Bruch
- Section for Translational Surgical Oncology & BiobankingDepartment of SurgeryUniversity of LübeckLübeckGermany
| | - Ulf Hellman
- Ludwig Institute for Cancer ResearchLtd. UppsalaUppsalaSweden
| | - Thomas Ried
- Center for Cancer ResearchNational Cancer InstituteNIHBethesdaMDUSA
| | - Gert Auer
- Karolinska Biomic CenterKarolinska InstitutetStockholmSweden
| | - Hans Jörnvall
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
| | - Uwe J. Roblick
- Section for Translational Surgical Oncology & BiobankingDepartment of SurgeryUniversity of LübeckLübeckGermany
- Department of Medical Biochemistry and BiophysicsKarolinska InstitutetStockholmSweden
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Bünger S, Haug U, Kelly M, Posorski N, Klempt-Giessing K, Cartwright A, Fitzgerald SP, Toner V, McAleer D, Gemoll T, Laubert T, Büning J, Fellermann K, Bruch HP, Roblick UJ, Brenner H, von Eggeling F, Habermann JK. A novel multiplex-protein array for serum diagnostics of colon cancer: a case-control study. BMC Cancer 2012; 12:393. [PMID: 22954206 PMCID: PMC3502594 DOI: 10.1186/1471-2407-12-393] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [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: 05/11/2012] [Accepted: 08/31/2012] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND More than 1.2 million new cases of colorectal cancer are reported each year worldwide. Despite actual screening programs, about 50% of the patients are diagnosed at advanced tumor stages presenting poor prognosis. Innovative screening tools could aid the detection at early stages and allow curative treatment interventions. METHODS A nine target multiplex serum protein biochip was generated and evaluated using a training- and validation-set of 317 highly standardized, liquid nitrogen preserved serum samples comprising controls, adenomas, and colon cancers. RESULTS Serum levels of CEA, IL-8, VEGF, S100A11, MCSF, C3adesArg, CD26, and CRP showed significant differences between cases and controls. The largest areas under the receiver operating characteristics curve were observed for CEA, IL-8, and CRP. At threshold levels yielding 90% specificity, sensitivities for CEA, IL-8 and CRP were 26%, 22%, and 17%, respectively. The most promising marker combinations were CEA + IL-8 reaching 37% sensitivity at 83% specificity and CEA + CRP with 35% sensitivity at 81% specificity. In an independent validation set CEA + IL-8 reached 47% sensitivity at 86% specificity while CEA + CRP obtained 39% sensitivity at 86% specificity. Early carcinomas were detected with 33% sensitivity for CEA + IL-8 and 28% for CEA + CRP. CONCLUSIONS Apart from CEA, IL-8, and CRP, the screening value of additional blood markers and the potential advantage of combining serum biochip testing with fecal occult blood testing needs to be studied. Multiplex biochip array technology utilizing serum samples offers an innovative approach to colorectal cancer screening.
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Affiliation(s)
- Stefanie Bünger
- Laboratory for Surgical Research, Department of Surgery, University of Lübeck, Ratzeburger Allee 160, D-23538, Lübeck, Germany
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Laubert T, Habermann JK, Hemmelmann C, Kleemann M, Oevermann E, Bouchard R, Hildebrand P, Jungbluth T, Bürk C, Esnaashari H, Schlöricke E, Hoffmann M, Ziegler A, Bruch HP, Roblick UJ. Metachronous metastasis- and survival-analysis show prognostic importance of lymphadenectomy for colon carcinomas. BMC Gastroenterol 2012; 12:24. [PMID: 22443372 PMCID: PMC3349572 DOI: 10.1186/1471-230x-12-24] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/05/2011] [Accepted: 03/23/2012] [Indexed: 01/04/2023] Open
Abstract
Background Lymphadenectomy is performed to assess patient prognosis and to prevent metastasizing. Recently, it was questioned whether lymph node metastases were capable of metastasizing and therefore, if lymphadenectomy was still adequate. We evaluated whether the nodal status impacts on the occurrence of distant metastases by analyzing a highly selected cohort of colon cancer patients. Methods 1,395 patients underwent surgery exclusively for colon cancer at the University of Lübeck between 01/1993 and 12/2008. The following exclusion criteria were applied: synchronous metastasis, R1-resection, prior/synchronous second carcinoma, age < 50 years, positive family history, inflammatory bowel disease, FAP, HNPCC, and follow-up < 5 years. The remaining 421 patients were divided into groups with (TM+, n = 75) or without (TM-, n = 346) the occurrence of metastasis throughout a 5-year follow-up. Results Five-year survival rates for TM + and TM- were 21% and 73%, respectively (p < 0.0001). Survival rates differed significantly for N0 vs. N2, grading 2 vs. 3, UICC-I vs. -II and UICC-I vs. -III (p < 0.05). Regression analysis revealed higher age upon diagnosis, increasing N- and increasing T-category to significantly impact on recurrence free survival while increasing N-and T-category were significant parameters for the risk to develop metastases within 5-years after surgery (HR 1.97 and 1.78; p < 0.0001). Conclusions Besides a higher T-category, a positive N-stage independently implies a higher probability to develop distant metastases and correlates with poor survival. Our data thus show a prognostic relevance of lymphadenectomy which should therefore be retained until conclusive studies suggest the unimportance of lmyphadenectomy.
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Affiliation(s)
- Tilman Laubert
- Department of Surgery, Laboratory for Surgical Research, University of Lübeck, Ratzeburger Allee 160, D-23538 Lübeck, Germany.
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Prokosch HU, Mate S, Christoph J, Beck A, Köpcke F, Stephan S, Beckmann MW, Rau T, Hartmann A, Wullich B, Breil B, Eckardt KU, Titze S, Habermann JK, Ingenerf J, Hackmann M, Ries M, Bürkle T, Ganslandt T. Designing and implementing a biobanking IT framework for multiple research scenarios. Stud Health Technol Inform 2012; 180:559-563. [PMID: 22874253] [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] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
This paper presents a biobanking IT framework, comprising a set of integrated biobanking information technology components. It provides adaptable and scalable IT support for varying biobanking scenarios, workflows and projects, while avoiding redundancy in data and technology. Feasibility of this approach is illustrated by implementations for four different biobanking projects at Erlangen University Hospital and with cooperating partners in Münster and Lübeck.
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Habermann JK, Bündgen NK, Gemoll T, Hautaniemi S, Lundgren C, Wangsa D, Doering J, Bruch HP, Nordstroem B, Roblick UJ, Jörnvall H, Auer G, Ried T. Genomic instability influences the transcriptome and proteome in endometrial cancer subtypes. Mol Cancer 2011; 10:132. [PMID: 22040021 PMCID: PMC3261822 DOI: 10.1186/1476-4598-10-132] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [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: 07/23/2011] [Accepted: 10/31/2011] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND In addition to clinical characteristics, DNA aneuploidy has been identified as a prognostic factor in epithelial malignancies in general and in endometrial cancers in particular. We mapped ploidy-associated chromosomal aberrations and identified corresponding gene and protein expression changes in endometrial cancers of different prognostic subgroups. METHODS DNA image cytometry classified 25 endometrioid cancers to be either diploid (n = 16) or aneuploid (n = 9), and all uterine papillary serous cancers (UPSC) to be aneuploid (n = 8). All samples were subjected to comparative genomic hybridization and gene expression profiling. Identified genes were subjected to Ingenuity pathway analysis (IPA) and were correlated to protein expression changes. RESULTS Comparative genomic hybridization revealed ploidy-associated specific, recurrent genomic imbalances. Gene expression analysis identified 54 genes between diploid and aneuploid endometrioid carcinomas, 39 genes between aneuploid endometrioid cancer and UPSC, and 76 genes between diploid endometrioid and aneuploid UPSC to be differentially expressed. Protein profiling identified AKR7A2 and ANXA2 to show translational alterations consistent with the transcriptional changes. The majority of differentially expressed genes and proteins belonged to identical molecular functions, foremost Cancer, Cell Death, and Cellular Assembly and Organization. CONCLUSIONS We conclude that the grade of genomic instability rather than the histopathological subtype correlates with specific gene and protein expression changes. The identified genes and proteins might be useful as molecular targets for improved diagnostic and therapeutic intervention and merit prospective validation.
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Affiliation(s)
- Jens K Habermann
- Laboratory for Surgical Research, Department of Surgery, University of Lübeck, Germany.
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Petschnik AE, Fell B, Tiede S, Habermann JK, Pries R, Kruse C, Danner S. A novel xenogeneic co-culture system to examine neuronal differentiation capability of various adult human stem cells. PLoS One 2011; 6:e24944. [PMID: 21935488 PMCID: PMC3173484 DOI: 10.1371/journal.pone.0024944] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2011] [Accepted: 08/24/2011] [Indexed: 12/21/2022] Open
Abstract
Background Targeted differentiation of stem cells is mainly achieved by the sequential administration of defined growth factors and cytokines, although these approaches are quite artificial, cost-intensive and time-consuming. We now present a simple xenogeneic rat brain co-culture system which supports neuronal differentiation of adult human stem cells under more in vivo-like conditions. Methods and Findings This system was applied to well-characterized stem cell populations isolated from human skin, parotid gland and pancreas. In addition to general multi-lineage differentiation potential, these cells tend to differentiate spontaneously into neuronal cell types in vitro and are thus ideal candidates for the introduced co-culture system. Consequently, after two days of co-culture up to 12% of the cells showed neuronal morphology and expressed corresponding markers on the mRNA and protein level. Additionally, growth factors with the ability to induce neuronal differentiation in stem cells could be found in the media supernatants of the co-cultures. Conclusions The co-culture system described here is suitable for testing neuronal differentiation capability of numerous types of stem cells. Especially in the case of human cells, it may be of clinical relevance for future cell-based therapeutic applications.
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Affiliation(s)
- Anna E. Petschnik
- Fraunhofer Research Institution for Marine Biotechnology, Lübeck, Germany
| | - Benjamin Fell
- Fraunhofer Research Institution for Marine Biotechnology, Lübeck, Germany
| | - Stephan Tiede
- Department of Dermatology, Allergology and Venerology, University of Lübeck, Lübeck, Germany
| | | | - Ralph Pries
- ENT Department, University of Lübeck, Lübeck, Germany
| | - Charli Kruse
- Fraunhofer Research Institution for Marine Biotechnology, Lübeck, Germany
| | - Sandra Danner
- Fraunhofer Research Institution for Marine Biotechnology, Lübeck, Germany
- * E-mail:
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Gemoll T, Roblick UJ, Habermann JK. MALDI mass spectrometry imaging in oncology (Review). Mol Med Rep 2011; 4:1045-51. [PMID: 21874241 DOI: 10.3892/mmr.2011.566] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 08/09/2011] [Indexed: 11/06/2022] Open
Abstract
Matrix-assisted laser desorption/ionization (MALDI) mass spectrometry imaging (MSI) has improved over the years and is increasingly being used for biomarker discovery directly from human tissue sections. State-of-the-art technology currently enables a resolution down to 20 µm. MSI therefore allows the correlation of spatial and temporal protein expression profiles with distinct morphological features without requiring target-specific reagents, such as antibodies. Several studies have demonstrated the strength of the technology for uncovering new markers that correlate with disease severity as well as prognosis and therapeutic response. This review provides an overview of MALDI imaging functionality and its advantages and disadvantages, and provides a current literature overview of malignancy-based biomarker detection. Further improvements on instrumentation sensitivity, image processing and sample preparation will enable the detection of novel, tissue-specific biomarkers. However, emphasis should be given to large validation studies and/or subsequent identification of differentially observed protein peaks in order to transfer MSI protein profiling and/or novel biomarkers thereof into clinical use.
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Affiliation(s)
- Timo Gemoll
- Department of Surgery, Laboratory for Surgical Research, University of Lübeck, D-23538 Lübeck, Germany
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Gerling M, Glauben R, Habermann JK, Kühl AA, Loddenkemper C, Lehr HA, Zeitz M, Siegmund B. Characterization of chromosomal instability in murine colitis-associated colorectal cancer. PLoS One 2011; 6:e22114. [PMID: 21799775 PMCID: PMC3142131 DOI: 10.1371/journal.pone.0022114] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2011] [Accepted: 06/16/2011] [Indexed: 12/27/2022] Open
Abstract
Background Patients suffering from ulcerative colitis (UC) bear an increased risk for colorectal cancer. Due to the sparsity of colitis-associated cancer (CAC) and the long duration between UC initiation and overt carcinoma, elucidating mechanisms of inflammation-associated carcinogenesis in the gut is particularly challenging. Adequate murine models are thus highly desirable. For human CACs a high frequency of chromosomal instability (CIN) reflected by aneuploidy could be shown, exceeding that of sporadic carcinomas. The aim of this study was to analyze mouse models of CAC with regard to CIN. Additionally, protein expression of p53, beta-catenin and Ki67 was measured to further characterize murine tumor development in comparison to UC-associated carcinogenesis in men. Methods The AOM/DSS model (n = 23) and IL-10−/− mice (n = 8) were applied to monitor malignancy development via endoscopy and to analyze premalignant and malignant stages of CACs. CIN was assessed using DNA-image cytometry. Protein expression of p53, beta-catenin and Ki67 was evaluated by immunohistochemistry. The degree of inflammation was analyzed by histology and paralleled to local interferon-γ release. Results CIN was detected in 81.25% of all murine CACs induced by AOM/DSS, while all carcinomas that arose in IL-10−/− mice were chromosomally stable. Beta-catenin expression was strongly membranous in IL-10−/− mice, while 87.50% of AOM/DSS-induced tumors showed cytoplasmatic and/or nuclear translocation of beta-catenin. p53 expression was high in both models and Ki67 staining revealed higher proliferation of IL-10−/−-induced CACs. Conclusions AOM/DSS-colitis, but not IL-10−/− mice, could provide a powerful murine model to mechanistically investigate CIN in colitis-associated carcinogenesis.
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Affiliation(s)
- Marco Gerling
- Medical Clinic I, Charité-Universitätsmedizin Berlin, Campus Benjamin Franklin, Berlin, Germany.
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