1
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Zhong Q, Sun R, Aref AT, Noor Z, Anees A, Zhu Y, Lucas N, Poulos RC, Lyu M, Zhu T, Chen GB, Wang Y, Ding X, Rutishauser D, Rupp NJ, Rueschoff JH, Poyet C, Hermanns T, Fankhauser C, Rodríguez Martínez M, Shao W, Buljan M, Neumann JF, Beyer A, Hains PG, Reddel RR, Robinson PJ, Aebersold R, Guo T, Wild PJ. Proteomic-based stratification of intermediate-risk prostate cancer patients. Life Sci Alliance 2024; 7:e202302146. [PMID: 38052461 PMCID: PMC10698198 DOI: 10.26508/lsa.202302146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Revised: 11/22/2023] [Accepted: 11/23/2023] [Indexed: 12/07/2023] Open
Abstract
Gleason grading is an important prognostic indicator for prostate adenocarcinoma and is crucial for patient treatment decisions. However, intermediate-risk patients diagnosed in the Gleason grade group (GG) 2 and GG3 can harbour either aggressive or non-aggressive disease, resulting in under- or overtreatment of a significant number of patients. Here, we performed proteomic, differential expression, machine learning, and survival analyses for 1,348 matched tumour and benign sample runs from 278 patients. Three proteins (F5, TMEM126B, and EARS2) were identified as candidate biomarkers in patients with biochemical recurrence. Multivariate Cox regression yielded 18 proteins, from which a risk score was constructed to dichotomize prostate cancer patients into low- and high-risk groups. This 18-protein signature is prognostic for the risk of biochemical recurrence and completely independent of the intermediate GG. Our results suggest that markers generated by computational proteomic profiling have the potential for clinical applications including integration into prostate cancer management.
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Affiliation(s)
- Qing Zhong
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Rui Sun
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Adel T Aref
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Zainab Noor
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Asim Anees
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Yi Zhu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Natasha Lucas
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Rebecca C Poulos
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Mengge Lyu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Tiansheng Zhu
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Guo-Bo Chen
- Urology & Nephrology Center, Department of Urology, Clinical Research Institute, Zhejiang Provincial People's Hospital, People's Hospital of Hangzhou Medical College, Hangzhou, China
| | - Yingrui Wang
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Xuan Ding
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Dorothea Rutishauser
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Niels J Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Jan H Rueschoff
- Department of Pathology and Molecular Pathology, University Hospital Zürich, Zürich, Switzerland
| | - Cédric Poyet
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
| | - Thomas Hermanns
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
| | - Christian Fankhauser
- Department of Urology, University Hospital Zürich, Zürich, Switzerland
- Department of Urology, Cantonal Hospital Lucerne, Lucerne, Switzerland
| | | | - Wenguang Shao
- State Key Laboratory of Microbial Metabolism, Joint International Research Laboratory of Metabolic and Developmental Sciences, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai, China
| | - Marija Buljan
- Empa - Swiss Federal Laboratories for Materials Science and Technology, St. Gallen, Switzerland
- Swiss Institute of Bioinformatics, Lausanne, Switzerland
| | | | | | - Peter G Hains
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Roger R Reddel
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Phillip J Robinson
- https://ror.org/01bsaey45 ProCan, Children's Medical Research Institute, Faculty of Medicine and Health, The University of Sydney, Westmead, Australia
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zürich, Zürich, Switzerland
- Faculty of Science, University of Zürich, Zürich, Switzerland
| | - Tiannan Guo
- https://ror.org/05hfa4n20 iMarker Lab, Westlake Laboratory of Life Sciences and Biomedicine, Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, Hangzhou, China
- Institute of Basic Medical Sciences, Westlake Institute for Advanced Study, Hangzhou, China
| | - Peter J Wild
- Goethe University Frankfurt, Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt am Main, Germany
- Frankfurt Institute for Advanced Studies, Frankfurt am Main, Germany
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2
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Brina D, Ponzoni A, Troiani M, Calì B, Pasquini E, Attanasio G, Mosole S, Mirenda M, D'Ambrosio M, Colucci M, Guccini I, Revandkar A, Alajati A, Tebaldi T, Donzel D, Lauria F, Parhizgari N, Valdata A, Maddalena M, Calcinotto A, Bolis M, Rinaldi A, Barry S, Rüschoff JH, Sabbadin M, Sumanasuriya S, Crespo M, Sharp A, Yuan W, Grinu M, Boyle A, Miller C, Trotman L, Delaleu N, Fassan M, Moch H, Viero G, de Bono J, Alimonti A. The Akt/mTOR and MNK/eIF4E pathways rewire the prostate cancer translatome to secrete HGF, SPP1 and BGN and recruit suppressive myeloid cells. NATURE CANCER 2023; 4:1102-1121. [PMID: 37460872 PMCID: PMC11331482 DOI: 10.1038/s43018-023-00594-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/09/2022] [Accepted: 06/13/2023] [Indexed: 08/25/2023]
Abstract
Cancer is highly infiltrated by myeloid-derived suppressor cells (MDSCs). Currently available immunotherapies do not completely eradicate MDSCs. Through a genome-wide analysis of the translatome of prostate cancers driven by different genetic alterations, we demonstrate that prostate cancer rewires its secretome at the translational level to recruit MDSCs. Among different secreted proteins released by prostate tumor cells, we identified Hgf, Spp1 and Bgn as the key factors that regulate MDSC migration. Mechanistically, we found that the coordinated loss of Pdcd4 and activation of the MNK/eIF4E pathways regulate the mRNAs translation of Hgf, Spp1 and Bgn. MDSC infiltration and tumor growth were dampened in prostate cancer treated with the MNK1/2 inhibitor eFT508 and/or the AKT inhibitor ipatasertib, either alone or in combination with a clinically available MDSC-targeting immunotherapy. This work provides a therapeutic strategy that combines translation inhibition with available immunotherapies to restore immune surveillance in prostate cancer.
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Affiliation(s)
- Daniela Brina
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Adele Ponzoni
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Ima Biotech, Lille, France
| | - Martina Troiani
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
| | - Bianca Calì
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Emiliano Pasquini
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Giuseppe Attanasio
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Simone Mosole
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Michela Mirenda
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Evotec, Toulouse, France
| | - Mariantonietta D'Ambrosio
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Imperial College London, London, UK
| | - Manuel Colucci
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Ilaria Guccini
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Institute of Molecular Health Sciences, ETH Zurich, Zurich, Switzerland
| | - Ajinkya Revandkar
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Harvard Medical School, Massachusetts General Hospital Cancer Center, Boston, MA, USA
| | - Abdullah Alajati
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Department of Urology, Universitätklinikum Bonn, Bonn, Germany
| | - Toma Tebaldi
- Yale Cancer Center and Department of Internal Medicine, Yale University School of Medicine, New Haven, CT, USA
| | - Deborah Donzel
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Fabio Lauria
- Institute of Biophysics, CNR Unit at Trento, Povo, Italy
| | - Nahjme Parhizgari
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
- Biosun Pharmed, Kordan, Iran
| | - Aurora Valdata
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Martino Maddalena
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Arianna Calcinotto
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Marco Bolis
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland
- Bioinformatics Core Unit, Swiss Institute of Bioinformatics, Bellinzona, Switzerland
- Computational Oncology Unit, Department of Oncology, Istituto di Richerche Farmacologiche 'Mario Negri' IRCCS, Milano, Italy
| | - Andrea Rinaldi
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland
| | - Simon Barry
- IMED Oncology AstraZeneca, Li Ka Shing Centre, Cambridge, UK
| | - Jan Hendrik Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Semini Sumanasuriya
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Mateus Crespo
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Adam Sharp
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Wei Yuan
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
| | - Mathew Grinu
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Alexandra Boyle
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Cynthia Miller
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | - Lloyd Trotman
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, NY, USA
| | | | - Matteo Fassan
- Veneto Institute of Oncology, IOV-IRCCS, Padua, Italy
- Department of Medicine (DIMED), Surgical Pathology Unit, University of Padua, Padua, Italy
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich, Switzerland
| | | | - Johann de Bono
- Institute of Cancer Research and Royal Marsden NHS Foundation Trust, London, UK
- The Royal Marsden Hospital, London, UK
| | - Andrea Alimonti
- Institute of Oncology Research, Oncology Institute of Southern Switzerland, Bellinzona, Switzerland.
- Faculty of Biomedical Sciences, Università della Svizzera Italiana, Lugano, Switzerland.
- Department of Medicine, Venetian Institute of Molecular Medicine, University of Padova, Padova, Italy.
- Department of Health Sciences and Technology, Eidgenössische Technische Hochschule (ETH) Zürich, Zurich, Switzerland.
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3
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Milewski D, Jung H, Brown GT, Liu Y, Somerville B, Lisle C, Ladanyi M, Rudzinski ER, Choo-Wosoba H, Barkauskas DA, Lo T, Hall D, Linardic CM, Wei JS, Chou HC, Skapek SX, Venkatramani R, Bode PK, Steinberg SM, Zaki G, Kuznetsov IB, Hawkins DS, Shern JF, Collins J, Khan J. Predicting Molecular Subtype and Survival of Rhabdomyosarcoma Patients Using Deep Learning of H&E Images: A Report from the Children's Oncology Group. Clin Cancer Res 2023; 29:364-378. [PMID: 36346688 PMCID: PMC9843436 DOI: 10.1158/1078-0432.ccr-22-1663] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 08/01/2022] [Accepted: 11/02/2022] [Indexed: 11/09/2022]
Abstract
PURPOSE Rhabdomyosarcoma (RMS) is an aggressive soft-tissue sarcoma, which primarily occurs in children and young adults. We previously reported specific genomic alterations in RMS, which strongly correlated with survival; however, predicting these mutations or high-risk disease at diagnosis remains a significant challenge. In this study, we utilized convolutional neural networks (CNN) to learn histologic features associated with driver mutations and outcome using hematoxylin and eosin (H&E) images of RMS. EXPERIMENTAL DESIGN Digital whole slide H&E images were collected from clinically annotated diagnostic tumor samples from 321 patients with RMS enrolled in Children's Oncology Group (COG) trials (1998-2017). Patches were extracted and fed into deep learning CNNs to learn features associated with mutations and relative event-free survival risk. The performance of the trained models was evaluated against independent test sample data (n = 136) or holdout test data. RESULTS The trained CNN could accurately classify alveolar RMS, a high-risk subtype associated with PAX3/7-FOXO1 fusion genes, with an ROC of 0.85 on an independent test dataset. CNN models trained on mutationally-annotated samples identified tumors with RAS pathway with a ROC of 0.67, and high-risk mutations in MYOD1 or TP53 with a ROC of 0.97 and 0.63, respectively. Remarkably, CNN models were superior in predicting event-free and overall survival compared with current molecular-clinical risk stratification. CONCLUSIONS This study demonstrates that high-risk features, including those associated with certain mutations, can be readily identified at diagnosis using deep learning. CNNs are a powerful tool for diagnostic and prognostic prediction of rhabdomyosarcoma, which will be tested in prospective COG clinical trials.
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Affiliation(s)
| | - Hyun Jung
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - G. Thomas Brown
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
- Artificial Intelligence Resource, NCI, NIH, Bethesda, Maryland
| | - Yanling Liu
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | | | - Curtis Lisle
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
- KnowledgeVis, LLC, Altamonte Springs, Florida
| | - Marc Ladanyi
- Department of Pathology, Memorial Sloan-Kettering Cancer Center, New York, New York
| | - Erin R. Rudzinski
- Department of Laboratories, Seattle Children's Hospital, Seattle, Washington
| | - Hyoyoung Choo-Wosoba
- Biostatistics and Data Management Section, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - Donald A. Barkauskas
- Department of Population and Public Health Sciences, Keck School of Medicine of the University of Southern California, Los Angeles, California
- Children's Oncology Group, Monrovia, California
| | - Tammy Lo
- Children's Oncology Group, Monrovia, California
| | - David Hall
- Children's Oncology Group, Monrovia, California
| | - Corinne M. Linardic
- Departments of Pediatrics and Pharmacology & Cancer Biology, Duke University School of Medicine, Durham, North Carolina
| | - Jun S. Wei
- Genetics Branch, NCI, NIH, Bethesda, Maryland
| | | | - Stephen X. Skapek
- Department of Pediatrics, Division of Hematology/Oncology, University of Texas Southwestern Medical Center, Dallas, Texas
| | - Rajkumar Venkatramani
- Division of Hematology/Oncology, Texas Children's Cancer Center, Baylor College of Medicine, Houston, Texas
| | - Peter K. Bode
- Institut für Pathologie, Kantonsspital Winterthur, Winterthur, Switzerland
| | - Seth M. Steinberg
- Biostatistics and Data Management Section, Keck School of Medicine of the University of Southern California, Los Angeles, California
| | - George Zaki
- Cancer Research Technology Program, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Igor B. Kuznetsov
- Department of Epidemiology & Biostatistics, School of Public Health, University at Albany, Rensselaer, New York
| | - Douglas S. Hawkins
- Chair of Children's Oncology Group, Department of Pediatrics, Seattle Children's Hospital, Fred Hutchinson Cancer Research Center, University of Washington, Seattle, Washington
| | - Jack F. Shern
- Pediatric Oncology Branch, Center for Cancer Research, NIH, Bethesda, Maryland
| | - Jack Collins
- Advanced Biomedical Computational Science, Frederick National Laboratory for Cancer Research, Frederick, Maryland
| | - Javed Khan
- Genetics Branch, NCI, NIH, Bethesda, Maryland
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4
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Breast Cancer Heterogeneity. Diagnostics (Basel) 2021; 11:diagnostics11091555. [PMID: 34573897 PMCID: PMC8468623 DOI: 10.3390/diagnostics11091555] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2021] [Revised: 08/22/2021] [Accepted: 08/26/2021] [Indexed: 01/22/2023] Open
Abstract
Breast tumor heterogeneity is a major challenge in the clinical management of breast cancer patients. Both inter-tumor and intra-tumor heterogeneity imply that each breast cancer (BC) could have different prognosis and would benefit from specific therapy. Breast cancer is a dynamic entity, changing during tumor progression and metastatization and this poses fundamental issues to the feasibility of a personalized medicine approach. The most effective therapeutic strategy for patients with recurrent disease should be assessed evaluating biopsies obtained from metastatic sites. Furthermore, the tumor progression and the treatment response should be strictly followed and radiogenomics and liquid biopsy might be valuable tools to assess BC heterogeneity in a non-invasive way.
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5
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Lee GS, Jeong HY, Yang HG, Seo YR, Jung EG, Lee YS, Nam KW, Kim WJ. Astragaloside IV Suppresses Hepatic Proliferation in Regenerating Rat Liver after 70% Partial Hepatectomy via Down-Regulation of Cell Cycle Pathway and DNA Replication. Molecules 2021; 26:2895. [PMID: 34068164 PMCID: PMC8152973 DOI: 10.3390/molecules26102895] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2021] [Revised: 05/06/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Astragaloside IV (AS-IV) is one of the major bio-active ingredients of huang qi which is the dried root of Astragalus membranaceus (a traditional Chinese medicinal plant). The pharmacological effects of AS-IV, including anti-oxidative, anti-cancer, and anti-diabetic effects have been actively studied, however, the effects of AS-IV on liver regeneration have not yet been fully described. Thus, the aim of this study was to explore the effects of AS-IV on regenerating liver after 70% partial hepatectomy (PHx) in rats. Differentially expressed mRNAs, proliferative marker and growth factors were analyzed. AS-IV (10 mg/kg) was administrated orally 2 h before surgery. We found 20 core genes showed effects of AS-IV, many of which were involved with functions related to DNA replication during cell division. AS-IV down-regulates MAPK signaling, PI3/Akt signaling, and cell cycle pathway. Hepatocyte growth factor (HGF) and cyclin D1 expression were also decreased by AS-IV administration. Transforming growth factor β1 (TGFβ1, growth regulation signal) was slightly increased. In short, AS-IV down-regulated proliferative signals and genes related to DNA replication. In conclusion, AS-IV showed anti-proliferative activity in regenerating liver tissue after 70% PHx.
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Affiliation(s)
- Gyeong-Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Korea; (G.-S.L.); (H.-Y.J.); (Y.-R.S.); (Y.-S.L.); (K.-W.N.)
| | - Hee-Yeon Jeong
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Korea; (G.-S.L.); (H.-Y.J.); (Y.-R.S.); (Y.-S.L.); (K.-W.N.)
| | - Hyeon-Gung Yang
- Soonchunhyang Institute of Medi-bio Science (SIMS), Soonchunhyang University, Cheonan 31151, Chungcheongnam-do, Korea;
| | - Young-Ran Seo
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Korea; (G.-S.L.); (H.-Y.J.); (Y.-R.S.); (Y.-S.L.); (K.-W.N.)
| | - Eui-Gil Jung
- Seoul Center, Korea Basic Science Institute, Seoul 02855, Korea;
| | - Yong-Seok Lee
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Korea; (G.-S.L.); (H.-Y.J.); (Y.-R.S.); (Y.-S.L.); (K.-W.N.)
| | - Kung-Woo Nam
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Korea; (G.-S.L.); (H.-Y.J.); (Y.-R.S.); (Y.-S.L.); (K.-W.N.)
| | - Wan-Jong Kim
- Department of Life Science and Biotechnology, College of Natural Sciences, Soonchunhyang University, Asan 31538, Chungcheongnam-do, Korea; (G.-S.L.); (H.-Y.J.); (Y.-R.S.); (Y.-S.L.); (K.-W.N.)
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6
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Guccini I, Revandkar A, D'Ambrosio M, Colucci M, Pasquini E, Mosole S, Troiani M, Brina D, Sheibani-Tezerji R, Elia AR, Rinaldi A, Pernigoni N, Rüschoff JH, Dettwiler S, De Marzo AM, Antonarakis ES, Borrelli C, Moor AE, Garcia-Escudero R, Alajati A, Attanasio G, Losa M, Moch H, Wild P, Egger G, Alimonti A. Senescence Reprogramming by TIMP1 Deficiency Promotes Prostate Cancer Metastasis. Cancer Cell 2021; 39:68-82.e9. [PMID: 33186519 DOI: 10.1016/j.ccell.2020.10.012] [Citation(s) in RCA: 51] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/25/2020] [Revised: 09/12/2020] [Accepted: 10/09/2020] [Indexed: 12/20/2022]
Abstract
Metastases account for most cancer-related deaths, yet the mechanisms underlying metastatic spread remain poorly understood. Recent evidence demonstrates that senescent cells, while initially restricting tumorigenesis, can induce tumor progression. Here, we identify the metalloproteinase inhibitor TIMP1 as a molecular switch that determines the effects of senescence in prostate cancer. Senescence driven either by PTEN deficiency or chemotherapy limits the progression of prostate cancer in mice. TIMP1 deletion allows senescence to promote metastasis, and elimination of senescent cells with a senolytic BCL-2 inhibitor impairs metastasis. Mechanistically, TIMP1 loss reprograms the senescence-associated secretory phenotype (SASP) of senescent tumor cells through activation of matrix metalloproteinases (MMPs). Loss of PTEN and TIMP1 in prostate cancer is frequent and correlates with resistance to docetaxel and worst clinical outcomes in patients treated in an adjuvant setting. Altogether, these findings provide insights into the dual roles of tumor-associated senescence and can potentially impact the treatment of prostate cancer.
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Affiliation(s)
- Ilaria Guccini
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Institute of Molecular Health Sciences, ETH Zurich, Zurich 8093, Switzerland
| | - Ajinkya Revandkar
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Mariantonietta D'Ambrosio
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Faculty of Biology and Medicine, University of Lausanne UNIL, Lausanne 1011, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Manuel Colucci
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Faculty of Biology and Medicine, University of Lausanne UNIL, Lausanne 1011, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Emiliano Pasquini
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Simone Mosole
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Martina Troiani
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Daniela Brina
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | | | - Angela Rita Elia
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Andrea Rinaldi
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Nicolò Pernigoni
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Jan Hendrik Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich 8091, Switzerland
| | - Susanne Dettwiler
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich 8091, Switzerland
| | - Angelo M De Marzo
- Departments of Pathology, Urology and Oncology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21231, USA
| | - Emmanuel S Antonarakis
- Departments of Oncology and Urology, Sidney Kimmel Comprehensive Cancer Center, The Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Costanza Borrelli
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Andreas E Moor
- Department of Biosystems Science and Engineering, ETH Zurich, Basel 4058, Switzerland
| | - Ramon Garcia-Escudero
- Molecular Oncology Unit, CIEMAT, Madrid 28040, Spain; Biomedicine Research Institute, Hospital 12 Octubre, Madrid 28041, Spain; CIBERONC, Madrid 28029, Spain
| | - Abdullah Alajati
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Giuseppe Attanasio
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland
| | - Marco Losa
- Anatomical Pathology Specialization Unit, Toma Advanced Biomedical Assay, Busto Arsizio 21052, Italy
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich (USZ), Zurich 8091, Switzerland
| | - Peter Wild
- Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, 60596 Frankfurt Am Main, Germany; Frankfurt Institute for Advanced Studies (FIAS), Frankfurt 60438, Germany
| | - Gerda Egger
- Ludwig Boltzmann Institute Applied Diagnostics, 1090 Vienna, Austria; Department of Pathology, Medical University of Vienna, 1090 Vienna, Austria
| | - Andrea Alimonti
- Institute of Oncology Research (IOR), Oncology Institute of Southern Switzerland (IOSI), Bellinzona 6500, Switzerland; Università della Svizzera Italiana, Lugano 6900, Switzerland; Department of Medicine, University of Padua, Padua 35128, Italy; Department of Health Sciences and Technology (D-HEST) ETH Zurich, Zurich 8093, Switzerland.
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7
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Cross-Platform Comparison of Computer-assisted Image Analysis Quantification of In Situ mRNA Hybridization in Investigative Pathology. Appl Immunohistochem Mol Morphol 2020; 27:15-26. [PMID: 28682833 DOI: 10.1097/pai.0000000000000542] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Although availability of automated platforms has proliferated, there is no standard practice for computer-assisted generation of scores for mRNA in situ hybridization (ISH) visualized by brightfield microscopic imaging on tissue sections. To address this systematically, an ISH for peptidylprolyl isomerase B (PPIB) (cyclophilin B) mRNA was optimized and applied to a tissue microarray of archival non-small cell lung carcinoma cases, and then automated image analysis for PPIB was refined across 4 commercially available software platforms. Operator experience and scoring results from ImageScope, HALO, CellMap, and Developer XD were systematically compared with each other and to manual pathologist scoring. Markup images were compared and contrasted for accuracy, the ability of the platform to identify cells, and the ease of visual assessment to determine appropriate interpretation. Comparing weighted scoring approaches using H-scores (Developer XD, ImageScope, and manual scoring) a correlation was observed (R value=0.7955), and association between the remaining 2 approaches (HALO and CellMap) was of similar value. ImageScope showed the highest R value in comparison with manual scoring (0.7377). Mean-difference plots showed that HALO produced the highest relative normalized values, suggesting higher relative sensitivity. ImageScope overestimated PPIB ISH signal at the high end of the range scores; however, this tendency was not observed in other platforms. HALO emerged with the highest number of favorable observations, no apparent systematic bias in score generation compared with the other methods, and potentially higher sensitivity to detect ISH. HALO may serve as a tool to empower teams of investigative pathology laboratory scientists to assist pathologists readily with quantitative scoring of ISH.
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8
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Turnquist C, Watson RA, Protheroe A, Verrill C, Sivakumar S. Tumor heterogeneity: does it matter? Expert Rev Anticancer Ther 2019; 19:857-867. [PMID: 31510810 DOI: 10.1080/14737140.2019.1667236] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Introduction: It has long been recognized that tumors are composed of a mosaic of cells and numerous methods have been developed to detect tumor heterogeneity, including in situ hybridization, multi-regional sampling, cytological assays, and whole genome and single cell sequencing. Using these methods, heterogeneity has been observed at the genetic, epigenetic, and phenotypic level in numerous cancers. With the advent of deep sequencing technology, we now appreciate a greater complexity of distinct genotypes and phenotypes that drive the biological behavior of cancer. Despite decades of progress in detecting tumor heterogeneity, the question remains: to what extent does it matter? Areas covered: This review explores the evidence for and against the importance of tumor heterogeneity in three main areas: prognostication, development of targeted therapeutics and tumor resistance; summarizing current understanding before evaluating ongoing experimental and clinical developments. Expert opinion: Theoretical understanding and in vitro detection of intratumour heterogeneity promises much but is yet to translate into meaningful clinical benefit. However, the recent emergence of a host of technological innovations and upcoming clinical trials may soon change the landscape of this field.
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Affiliation(s)
- Casmir Turnquist
- University of Oxford Medical School, John Radcliffe Hospital , Oxford , UK
| | | | | | - Clare Verrill
- Nuffield Department of Surgical Sciences, Oxford NIHR Biomedical Research Centre , Oxford , UK
| | - Shivan Sivakumar
- Department of Oncology, University of Oxford , Oxford , UK.,Kennedy Institute of Rheumatology, University of Oxford , Oxford , UK
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9
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High-content, cell-by-cell assessment of HER2 overexpression and amplification: a tool for intratumoral heterogeneity detection in breast cancer. J Transl Med 2019; 99:722-732. [PMID: 30659272 PMCID: PMC6522386 DOI: 10.1038/s41374-018-0172-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2018] [Revised: 12/04/2018] [Accepted: 12/04/2018] [Indexed: 01/25/2023] Open
Abstract
Immunohistochemistry and fluorescence in situ hybridization are the two standard methods for human epidermal growth factor receptor 2 (HER2) assessment. However, they have severe limitations to assess quantitatively intratumoral heterogeneity (ITH) when multiple subclones of tumor cells co-exist. We develop here a high-content, quantitative analysis of breast cancer tissues based on microfluidic experimentation and image processing, to characterize both HER2 protein overexpression and HER2 gene amplification at the cellular level. The technique consists of performing sequential steps on the same tissue slide: an immunofluorescence (IF) assay using a microfluidic protocol, an elution step for removing the IF staining agents, a standard FISH staining protocol, followed by automated quantitative cell-by-cell image processing. Moreover, ITH is accurately detected in both cluster and mosaic form using an analysis of spatial association and a mathematical model that allows discriminating true heterogeneity from artifacts due to the use of thin tissue sections. This study paves the way to evaluate ITH with high accuracy and content while requiring standard staining methods.
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10
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Aziz D, Etemadmoghadam D, Caldon CE, Au-Yeung G, Deng N, Hutchinson R, Bowtell D, Waring P. 19q12 amplified and non-amplified subsets of high grade serous ovarian cancer with overexpression of cyclin E1 differ in their molecular drivers and clinical outcomes. Gynecol Oncol 2018; 151:327-336. [PMID: 30209015 DOI: 10.1016/j.ygyno.2018.08.039] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2018] [Revised: 08/24/2018] [Accepted: 08/27/2018] [Indexed: 10/28/2022]
Abstract
OBJECTIVES Readily apparent cyclin E1 expression occurs in 50% of HGSOC, but only half are linked to 19q12 locus amplification. The amplified/cyclin E1hi subset has intact BRCA1/2, unfavorable outcome, and is potentially therapeutically targetable. We studied whether non-amplified/cyclin E1hi HGSOC has similar characteristics. We also assessed the expression of cyclin E1 degradation-associated proteins, FBXW7 and USP28, as potential drivers of high cyclin E1 expression in both subsets. METHODS 262 HGSOC cases were analyzed by in situ hybridization for 19q12 locus amplification and immunohistochemistry for cyclin E1, URI1 (another protein encoded by the 19q12 locus), FBXW7 and USP28 expression. Tumors were classified by 19q12 amplification status and correlated to cyclin E1 and URI1 expression, BRCA1/2 germline mutation, FBXW7 and USP28 expression, and clinical outcomes. Additionally, we assessed the relative genomic instability of amplified/cyclin E1hi and non-amplified/cyclin E1hi groups of HGSOC datasets from The Cancer Genome Atlas. RESULTS Of the 82 cyclin E1hi cases, 43 (52%) were amplified and 39 (48%) were non-amplified. Unlike amplified tumors, non-amplified/cyclin E1hi tumor status was not mutually exclusive with gBRCA1/2 mutation. The non-amplified/cyclin E1hi group had significantly increased USP28, while the amplified/cyclin E1hi cancers had significantly lower FBXW7 expression consistent with a role for both in stabilizing cyclin E1. Notably, only the amplified/cyclin E1hi subset was associated with genomic instability and had a worse outcome than non-amplified/cyclin E1hi group. CONCLUSIONS Amplified/cyclin E1hi and non-amplified/cyclin E1hi tumors have different pathological and biological characteristics and clinical outcomes indicating that they are separate subsets of cyclin E1hi HGSOC.
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Affiliation(s)
- Diar Aziz
- Centre for Translational Pathology, Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia; Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Department of Surgery, University of Melbourne, Parkville, Victoria 3010, Australia
| | | | - C Elizabeth Caldon
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - George Au-Yeung
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - Niantao Deng
- The Kinghorn Cancer Centre, Garvan Institute of Medical Research, Darlinghurst, NSW 2010, Australia
| | - Ryan Hutchinson
- Centre for Translational Pathology, Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia
| | -
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia
| | - David Bowtell
- Peter MacCallum Cancer Centre, Melbourne, Victoria 3000, Australia; Sir Peter MacCallum Cancer Centre Department of Oncology, University of Melbourne, Parkville, Victoria, 3010, Australia.
| | - Paul Waring
- Centre for Translational Pathology, Department of Pathology, University of Melbourne, Parkville, Victoria 3010, Australia; Department of Surgery, University of Melbourne, Parkville, Victoria 3010, Australia.
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11
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Arvaniti E, Fricker KS, Moret M, Rupp N, Hermanns T, Fankhauser C, Wey N, Wild PJ, Rüschoff JH, Claassen M. Automated Gleason grading of prostate cancer tissue microarrays via deep learning. Sci Rep 2018; 8:12054. [PMID: 30104757 PMCID: PMC6089889 DOI: 10.1038/s41598-018-30535-1] [Citation(s) in RCA: 203] [Impact Index Per Article: 33.8] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2018] [Accepted: 07/19/2018] [Indexed: 12/31/2022] Open
Abstract
The Gleason grading system remains the most powerful prognostic predictor for patients with prostate cancer since the 1960s. Its application requires highly-trained pathologists, is tedious and yet suffers from limited inter-pathologist reproducibility, especially for the intermediate Gleason score 7. Automated annotation procedures constitute a viable solution to remedy these limitations. In this study, we present a deep learning approach for automated Gleason grading of prostate cancer tissue microarrays with Hematoxylin and Eosin (H&E) staining. Our system was trained using detailed Gleason annotations on a discovery cohort of 641 patients and was then evaluated on an independent test cohort of 245 patients annotated by two pathologists. On the test cohort, the inter-annotator agreements between the model and each pathologist, quantified via Cohen’s quadratic kappa statistic, were 0.75 and 0.71 respectively, comparable with the inter-pathologist agreement (kappa = 0.71). Furthermore, the model’s Gleason score assignments achieved pathology expert-level stratification of patients into prognostically distinct groups, on the basis of disease-specific survival data available for the test cohort. Overall, our study shows promising results regarding the applicability of deep learning-based solutions towards more objective and reproducible prostate cancer grading, especially for cases with heterogeneous Gleason patterns.
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Affiliation(s)
- Eirini Arvaniti
- Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland.,Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland
| | - Kim S Fricker
- Department of Pathology and Molecular Pathology, University of Zurich, Zurich, Switzerland
| | - Michael Moret
- Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland
| | - Niels Rupp
- Department of Pathology and Molecular Pathology, University of Zurich, Zurich, Switzerland
| | - Thomas Hermanns
- Department of Urology, University of Zurich, Zurich, Switzerland
| | | | - Norbert Wey
- Department of Pathology and Molecular Pathology, University of Zurich, Zurich, Switzerland
| | - Peter J Wild
- Department of Pathology and Molecular Pathology, University of Zurich, Zurich, Switzerland.,Dr. Senckenberg Institute of Pathology, University Hospital Frankfurt, Frankfurt, Germany
| | - Jan H Rüschoff
- Department of Pathology and Molecular Pathology, University of Zurich, Zurich, Switzerland.
| | - Manfred Claassen
- Institute for Molecular Systems Biology, ETH Zurich, Zurich, Switzerland. .,Swiss Institute of Bioinformatics (SIB), Zurich, Switzerland.
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12
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Pang F, Li H, Shi Y, Liu Z. Computational Analysis of Cell Dynamics in Videos with Hierarchical-Pooled Deep-Convolutional Features. J Comput Biol 2018; 25:934-953. [PMID: 29694245 PMCID: PMC6094353 DOI: 10.1089/cmb.2018.0023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Computational analysis of cellular appearance and its dynamics is used to investigate physiological properties of cells in biomedical research. In consideration of the great success of deep learning in video analysis, we first introduce two-stream convolutional networks (ConvNets) to automatically learn the biologically meaningful dynamics from raw live-cell videos. However, the two-stream ConvNets lack the ability to capture long-range video evolution. Therefore, a novel hierarchical pooling strategy is proposed to model the cell dynamics in a whole video, which is composed of trajectory pooling for short-term dynamics and rank pooling for long-range ones. Experimental results demonstrate that the proposed pipeline effectively captures the spatiotemporal dynamics from the raw live-cell videos and outperforms existing methods on our cell video database.
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Affiliation(s)
- Fengqian Pang
- Department of Information and Electronics, Beijing Institute of Technology, Beijing, China
| | - Heng Li
- Department of Information and Electronics, Beijing Institute of Technology, Beijing, China
| | - Yonggang Shi
- Department of Information and Electronics, Beijing Institute of Technology, Beijing, China
| | - Zhiwen Liu
- Department of Information and Electronics, Beijing Institute of Technology, Beijing, China
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13
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Joseph C, Papadaki A, Althobiti M, Alsaleem M, Aleskandarany MA, Rakha EA. Breast cancer intratumour heterogeneity: current status and clinical implications. Histopathology 2018; 73:717-731. [PMID: 29722058 DOI: 10.1111/his.13642] [Citation(s) in RCA: 47] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Breast cancer (BC) is a heterogeneous disease that varies in presentation, morphological features, behaviour, and response to therapy. High-throughput molecular profiling studies have revolutionised our understanding of BC heterogeneity, and have demonstrated that molecular profiles of tumours are variable not only between tumours, but also within individual tumours. Current evidence indicates that spatial and temporal intratumour heterogeneity of BC exists at levels beyond what are commonly expected. Intratumour heterogeneity poses critical challenges in the diagnosis, prediction of behaviour and management of BC. For instance, heterogeneous expression of oestrogen receptor, progesterone receptor and human epidermal growth factor receptor 2 can be seen not only in primary tumours between different regions, but also between primary tumours and their corresponding metastatic/recurrent lesions. The demonstration of molecularly distinct subclones within individual tumours may explain, at least in part, the mechanisms controlling the variable behaviour of BC, and may change our approach to BC sampling and treatment. In this review, BC intratumour heterogeneity is highlighted, with a special emphasis on the current knowledge pertaining to the relationship between intratumour heterogeneity and BC pathogenesis, evolution, and progression, with consideration of its impact on disease diagnosis, management, and the emergence of novel therapeutic targets. The key role of high-throughput molecular and imaging techniques is also addressed.
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Affiliation(s)
- Chitra Joseph
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Athanasia Papadaki
- Leicester Royal Infirmary, University Hospitals of Leicester NHS Trust, Leicester, UK
| | - Maryam Althobiti
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Mansour Alsaleem
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Mohammed A Aleskandarany
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK
| | - Emad A Rakha
- Academic Pathology, Division of Cancer and Stem Cells, School of Medicine, University of Nottingham, Nottingham City Hospital, Nottingham, UK.,Cellular Pathology, Nottingham University Hospitals NHS Trust, Nottingham, UK
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14
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Lin Z, Xu HN, Wang Y, Floros J, Li LZ. Differential Expression of PGC1α in Intratumor Redox Subpopulations of Breast Cancer. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2018; 1072:177-181. [PMID: 30178342 PMCID: PMC6429950 DOI: 10.1007/978-3-319-91287-5_28] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Our previous studies indicate that the mitochondrial redox state and its intratumor heterogeneity are associated with invasiveness and metastatic potential in human breast cancer cell models and mouse xenografts. To further study the molecular basis of redox heterogeneity, we obtained the fluorescence images of Fp (oxidized flavoproteins containing flavin adenine dinucleotide, i.e., FAD), NADH (reduced nicotinamide adenine dinucleotide), and the Fp redox ratio (FpR = Fp/(Fp + NADH)) of MDA-MB-231 xenografts by the Chance redox scanner, then isolated the intratumoral redox subpopulations by dissection according to the redox ratio image. A total of 12 subpopulations were isolated from 4 tumors (2-4 locations from each tumor). The 12 subpopulations were classified into 3 FpR groups: high FpR (HFpR, n = 4, FpR range 0.78-0.92, average 0.85), medium FpR (MFpR, n = 5, FpR range 0.39-0.68, average 0.52), and low FpR (LFpR, n = 3, FpR range 0.15-0.28, average 0.20). The RT-PCR (reverse transcription polymerase chain reaction) analysis on these redox subpopulations showed that PGC-1α is significantly upregulated in the HFpR redox group compared to the MFpR group (fold change 2.1, p = 0.008), but not significantly different between MFpR and LFpR groups, or between HFpR and LFpR groups. These results indicate that optical redox imaging (ORI)-based redox subpopulations exhibit differential expression of PGC1α gene and suggest that PGC1α might play a role in redox mediation of breast cancer progression.
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Affiliation(s)
- Zhenwu Lin
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - He N Xu
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA
| | - Yunhua Wang
- Department of Pediatrics, Pennsylvania State University, Hershey, PA, USA
| | - Joanna Floros
- Department of Pediatrics, Pennsylvania State University, Hershey, PA, USA
- Department of Obstetrics and Gynecology, College of Medicine, Pennsylvania State University, Hershey, PA, USA
| | - Lin Z Li
- Department of Radiology, Perelman School of Medicine, University of Pennsylvania, Philadelphia, PA, USA.
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15
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Graf JF, Zavodszky MI. Characterizing the heterogeneity of tumor tissues from spatially resolved molecular measures. PLoS One 2017; 12:e0188878. [PMID: 29190747 PMCID: PMC5708750 DOI: 10.1371/journal.pone.0188878] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2017] [Accepted: 11/14/2017] [Indexed: 11/18/2022] Open
Abstract
Background Tumor heterogeneity can manifest itself by sub-populations of cells having distinct phenotypic profiles expressed as diverse molecular, morphological and spatial distributions. This inherent heterogeneity poses challenges in terms of diagnosis, prognosis and efficient treatment. Consequently, tools and techniques are being developed to properly characterize and quantify tumor heterogeneity. Multiplexed immunofluorescence (MxIF) is one such technology that offers molecular insight into both inter-individual and intratumor heterogeneity. It enables the quantification of both the concentration and spatial distribution of 60+ proteins across a tissue section. Upon bioimage processing, protein expression data can be generated for each cell from a tissue field of view. Results The Multi-Omics Heterogeneity Analysis (MOHA) tool was developed to compute tissue heterogeneity metrics from MxIF spatially resolved tissue imaging data. This technique computes the molecular state of each cell in a sample based on a pathway or gene set. Spatial states are then computed based on the spatial arrangements of the cells as distinguished by their respective molecular states. MOHA computes tissue heterogeneity metrics from the distributions of these molecular and spatially defined states. A colorectal cancer cohort of approximately 700 subjects with MxIF data is presented to demonstrate the MOHA methodology. Within this dataset, statistically significant correlations were found between the intratumor AKT pathway state diversity and cancer stage and histological tumor grade. Furthermore, intratumor spatial diversity metrics were found to correlate with cancer recurrence. Conclusions MOHA provides a simple and robust approach to characterize molecular and spatial heterogeneity of tissues. Research projects that generate spatially resolved tissue imaging data can take full advantage of this useful technique. The MOHA algorithm is implemented as a freely available R script (see supplementary information).
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Affiliation(s)
- John F. Graf
- GE Global Research, Niskayuna, New York, United States of America
- * E-mail: (JFG); (MIZ)
| | - Maria I. Zavodszky
- GE Global Research, Niskayuna, New York, United States of America
- * E-mail: (JFG); (MIZ)
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16
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Detection of CCNE1/URI (19q12) amplification by in situ hybridisation is common in high grade and type II endometrial cancer. Oncotarget 2017; 8:14794-14805. [PMID: 27582547 PMCID: PMC5362444 DOI: 10.18632/oncotarget.11605] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2016] [Accepted: 08/13/2016] [Indexed: 12/21/2022] Open
Abstract
One TCGA subgroup of endometrial cancer (EC) is characterised by extensive genomic DNA copy number alterations. CCNE1 located at 19q12 is frequently amplified in EC and a target for anti-cancer therapy. The relevance of URI, also located at 19q12, is unknown. To evaluate the prevalence of 19q12 (CCNE1/URI) in EC, we investigated different histologic types by in situ hybridisation (ISH) and copy number assay. We applied a previously established 19q12 ISH for the detection of CCNE1/URI copy numbers in EC (n = 270) using conventional bright field microscopy. In a subset (n = 21), 19q12 amplification status was validated by OncoScan assay. Manual ISH was controlled by a recently developed computational ISHProfiler algorithm. Associations of 19q12 status with Cyclin E1, URI and p53 expression, and clinico-pathological parameters were tested. Amplification of 19q12 (CCNE1/URI) was found in 10.4% (28/270) and was significantly associated with type II EC (high grade and non-endometrioid; p < 0.0001), advanced FIGO stage (p = 0.001), high Cyclin E1 expression (p = 0.008) and aberrant p53 expression (p = 0.04). 19q12 ISH data were confirmed by OncoScan and computational ISHProfiler techniques. The 19q12 in situ hybridisation is a feasible and robust biomarker assay in molecular pathology. Amplification of CCNE1/URI predominantly occurred in type II endometrial cancer. Prospective clinical trials are warranted to assess the utility of combined 19q12 amplification and Cyclin E1/URI protein expression analysis for the prediction of therapeutic response to chemotherapy and/or cyclin-dependent kinase inhibitors in patients with endometrial cancer.
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17
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Prostate cancer-associated SPOP mutations confer resistance to BET inhibitors through stabilization of BRD4. Nat Med 2017; 23:1063-1071. [PMID: 28805820 PMCID: PMC5625299 DOI: 10.1038/nm.4378] [Citation(s) in RCA: 228] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 06/29/2017] [Indexed: 12/15/2022]
Abstract
The bromodomain and extra-terminal (BET) family of proteins, comprised of four members including BRD2, BRD3, BRD4 and the testis-specific isoform BRDT, largely function as transcriptional co-activators 1–3 and play critical roles in various cellular processes, including cell cycle, apoptosis, migration and invasion 4,5. As such, BET proteins enhance the oncogenic functions of major cancer drivers by either elevating their expression such as c-Myc in leukemia 6,7 or by promoting transcriptional activities of oncogenic factors such as AR and ERG in the prostate cancer setting 8. Pathologically, BET proteins are frequently overexpressed and clinically linked to various types of human cancers 5,9,10, therefore pursued as attractive therapeutic targets for selective inhibition in patients. To this end, a number of bromodomain inhibitors, including JQ1 and I-BET, have been developed 11,12 and shown promising outcomes in early clinical trials. Despite resistance to BET inhibitor has been documented in pre-clinical models 13–15 the molecular mechanisms underlying acquired resistance are largely unknown. Here, we report that Cullin 3SPOP earmarks BET proteins including BRD2, BRD3 and BRD4 for ubiquitination-mediated degradation. Pathologically, prostate cancer-associated SPOP mutants fail to interact with and promote the destruction of BET proteins, leading to their elevated abundance in SPOP-deficient prostate cancer. As a result, prostate cancer cells and prostate cancer patient-derived organoids harboring SPOP mutations are more resistant to BET inhibitor-induced cell growth arrest and apoptosis. Therefore, our results elucidate the tumor suppressor role of SPOP in prostate cancer by negatively controlling BET protein stability, and also provide a molecular mechanism for BET inhibitor resistance in prostate cancer patients bearing SPOP mutations.
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18
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Prostate cancer, PI3K, PTEN and prognosis. Clin Sci (Lond) 2017; 131:197-210. [PMID: 28057891 DOI: 10.1042/cs20160026] [Citation(s) in RCA: 125] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2016] [Revised: 11/12/2016] [Accepted: 11/21/2016] [Indexed: 12/22/2022]
Abstract
Loss of function of the PTEN tumour suppressor, resulting in dysregulated activation of the phosphoinositide 3-kinase (PI3K) signalling network, is recognized as one of the most common driving events in prostate cancer development. The observed mechanisms of PTEN loss are diverse, but both homozygous and heterozygous genomic deletions including PTEN are frequent, and often accompanied by loss of detectable protein as assessed by immunohistochemistry (IHC). The occurrence of PTEN loss is highest in aggressive metastatic disease and this has driven the development of PTEN as a prognostic biomarker, either alone or in combination with other factors, to distinguish indolent tumours from those likely to progress. Here, we discuss these factors and the consequences of PTEN loss, in the context of its role as a lipid phosphatase, as well as current efforts to use available inhibitors of specific components of the PI3K/PTEN/TOR signalling network in prostate cancer treatment.
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19
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Flanagan DJ, Vincan E, Phesse TJ. Winding back Wnt signalling: potential therapeutic targets for treating gastric cancers. Br J Pharmacol 2017; 174:4666-4683. [PMID: 28568899 DOI: 10.1111/bph.13890] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2017] [Revised: 05/17/2017] [Accepted: 05/22/2017] [Indexed: 12/21/2022] Open
Abstract
Gastric cancer persists as a frequent and deadly disease that claims over 700 000 lives annually. Gastric cancer is a multifactorial disease that is genetically, cytologically and architecturally more heterogeneous than other gastrointestinal cancers, making it therapeutically challenging. As such, and largely attributed to late-stage diagnosis, gastric cancer patients show only partial response to standard chemo and targeted molecular therapies, highlighting an urgent need to develop new targeted therapies for this disease. Wnt signalling has a well-documented history in the genesis of many cancers and is, therefore, an attractive therapeutic target. As such, drug discovery has focused on developing inhibitors that target multiple nodes of the Wnt signalling cascade, some of which have progressed to clinical trials. The collective efforts of patient genomic profiling has uncovered genetic lesions to multiple components of the Wnt pathway in gastric cancer patients, which strongly suggest that Wnt-targeted therapies could offer therapeutic benefits for gastric cancer patients. These data have been supported by studies in mouse models of gastric cancer, which identify Wnt signalling as a driver of gastric tumourigenesis. Here, we review the current literature regarding Wnt signalling in gastric cancer and highlight the suitability of each class of Wnt inhibitor as a potential treatment for gastric cancer patients, in relation to the type of Wnt deregulation observed. LINKED ARTICLES This article is part of a themed section on WNT Signalling: Mechanisms and Therapeutic Opportunities. To view the other articles in this section visit http://onlinelibrary.wiley.com/doi/10.1111/bph.v174.24/issuetoc.
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Affiliation(s)
- Dustin J Flanagan
- Molecular Oncology Laboratory, University of Melbourne, Melbourne, VIC, Australia.,Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia
| | - Elizabeth Vincan
- Molecular Oncology Laboratory, University of Melbourne, Melbourne, VIC, Australia.,Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia.,School of Biomedical Sciences, Curtin University, Perth, WA, Australia
| | - Toby J Phesse
- Molecular Oncology Laboratory, University of Melbourne, Melbourne, VIC, Australia.,Victorian Infectious Diseases Reference Laboratory, Doherty Institute of Infection and Immunity, Melbourne, VIC, Australia.,Cell Signalling and Cancer Laboratory, European Cancer Stem Cell Research Institute, Cardiff University, Cardiff, UK
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20
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Zhou H, Neelakantan D, Ford HL. Clonal cooperativity in heterogenous cancers. Semin Cell Dev Biol 2017; 64:79-89. [PMID: 27582427 PMCID: PMC5330947 DOI: 10.1016/j.semcdb.2016.08.028] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2016] [Accepted: 08/24/2016] [Indexed: 12/21/2022]
Abstract
Tumor heterogeneity is a major obstacle to the development of effective therapies and is thus an important focus of cancer research. Genetic and epigenetic alterations, as well as altered tumor microenvironments, result in tumors made up of diverse subclones with different genetic and phenotypic characteristics. Intratumor heterogeneity enables competition, but also supports clonal cooperation via cell-cell contact or secretion of factors, resulting in enhanced tumor progression. Here, we summarize recent findings related to interclonal interactions within a tumor and the therapeutic implications of such interactions, with an emphasis on how different subclones collaborate with each other to promote proliferation, metastasis and therapy-resistance. Furthermore, we propose that disruption of clonal cooperation by targeting key factors (such as Wnt and Hedgehog, amongst others) can be an alternative approach to improving clinical outcomes.
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Affiliation(s)
- Hengbo Zhou
- Program in Cancer Biology, University of Colorado School of Medicine, 12800 East 19th Avenue, Aurora, CO 80045, United States
| | - Deepika Neelakantan
- Program in Molecular Biology, University of Colorado School of Medicine, 12800 East 19th Avenue, Aurora, CO 80045, United States
| | - Heide L Ford
- Program in Cancer Biology, University of Colorado School of Medicine, 12800 East 19th Avenue, Aurora, CO 80045, United States; Program in Molecular Biology, University of Colorado School of Medicine, 12800 East 19th Avenue, Aurora, CO 80045, United States; Department of Pharmacology, University of Colorado School of Medicine, 12800 East 19th Avenue, Aurora, CO 80045, United States.
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21
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Zhong Q, Guo T, Rechsteiner M, Rüschoff JH, Rupp N, Fankhauser C, Saba K, Mortezavi A, Poyet C, Hermanns T, Zhu Y, Moch H, Aebersold R, Wild PJ. A curated collection of tissue microarray images and clinical outcome data of prostate cancer patients. Sci Data 2017; 4:170014. [PMID: 28291248 PMCID: PMC5349242 DOI: 10.1038/sdata.2017.14] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2016] [Accepted: 01/05/2017] [Indexed: 01/13/2023] Open
Abstract
Microscopy image data of human cancers provide detailed phenotypes of spatially and morphologically intact tissues at single-cell resolution, thus complementing large-scale molecular analyses, e.g., next generation sequencing or proteomic profiling. Here we describe a high-resolution tissue microarray (TMA) image dataset from a cohort of 71 prostate tissue samples, which was hybridized with bright-field dual colour chromogenic and silver in situ hybridization probes for the tumour suppressor gene PTEN. These tissue samples were digitized and supplemented with expert annotations, clinical information, statistical models of PTEN genetic status, and computer source codes. For validation, we constructed an additional TMA dataset for 424 prostate tissues, hybridized with FISH probes for PTEN, and performed survival analysis on a subset of 339 radical prostatectomy specimens with overall, disease-specific and recurrence-free survival (maximum 167 months). For application, we further produced 6,036 image patches derived from two whole slides. Our curated collection of prostate cancer data sets provides reuse potential for both biomedical and computational studies.
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Affiliation(s)
- Qing Zhong
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Tiannan Guo
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Markus Rechsteiner
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Jan H Rüschoff
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Niels Rupp
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | | | - Karim Saba
- Department of Urology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Ashkan Mortezavi
- Department of Urology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Cédric Poyet
- Department of Urology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Thomas Hermanns
- Department of Urology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Yi Zhu
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland
| | - Holger Moch
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland
| | - Ruedi Aebersold
- Department of Biology, Institute of Molecular Systems Biology, ETH Zurich, 8093 Zurich, Switzerland.,Faculty of Science, University of Zurich, 8057 Zurich, Switzerland
| | - Peter J Wild
- Department of Pathology and Molecular Pathology, University Hospital Zurich, 8091 Zurich, Switzerland.,University of Zurich, 8006 Zurich, Switzerland
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22
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Passerini V, Storchová Z. Too much to handle - how gaining chromosomes destabilizes the genome. Cell Cycle 2016; 15:2867-2874. [PMID: 27636196 PMCID: PMC5105935 DOI: 10.1080/15384101.2016.1231285] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2016] [Revised: 08/08/2016] [Accepted: 08/26/2016] [Indexed: 10/21/2022] Open
Abstract
Most eukaryotic organisms are diploid, with 2 chromosome sets in their nuclei. Whole chromosomal aneuploidy, a deviation from multiples of the haploid chromosome number, arises from chromosome segregation errors and often has detrimental consequences for cells. In humans, numerical aneuploidy severely impairs embryonic development and the rare survivors develop disorders characterized by multiple pathologies. Moreover, as many as 75 % of malignant tumors display aneuploidy. Although the exact contribution of aneuploidy to tumorigenesis remains unclear, previous studies have suggested that aneuploidy may affect the maintenance of genome integrity. We found that human cells with extra chromosomes showed phenotypes suggestive of replication defects, a phenomenon which we went on to characterize as being due to the aneuploidy-driven downregulation of replication factors, in particular of the replicative helicase MCM2-7. Thus, missegregation of even a single chromosome can further promote genomic instability and thereby contribute to tumor development. In this review we will examine the possible causes of downregulation of replicative factors and discuss the consequences of genomic instability in aneuploid cells.
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Affiliation(s)
- Verena Passerini
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
- Center for Integrated Protein Science, Ludwig-Maximilian-University, Munich, Germany
| | - Zuzana Storchová
- Group Maintenance of Genome Stability, Max Planck Institute of Biochemistry, Martinsried, Germany
- Center for Integrated Protein Science, Ludwig-Maximilian-University, Munich, Germany
- Technical University Kaiserslautern, Kaiserslautern, Germany
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