The Cancer Degradome

I. The Degradome and Its Analysis

1. Protease Genomics and the Cancer Degradome
Xose S. Puente, Gonzalo R. Ordóñez, Carlos López-Otín

2. The CLIP-CHIP™: A Focused Oligonucleotide Microarray Platform for Transcriptome Analysis of the Complete Human and Murine Cancer Degradomes
Reinhild Kappelhoff, Claire H. Wilson, Christopher M. Overall

3. The Hu/Mu ProtIn Chip: A Custom Dual-Species Oligonucleotide Microarray for Profiling Degradome Gene Expression in Tumors and Their Microenvironment
Donald R. Schwartz, Kamiar Moin, Ekkehard Weber, Bonnie F. Sloane

4. Quantitative Real-Time PCR Analysis of Degradome Gene Expression
Caroline J. Pennington, Robert K. Nuttall, Clara Sampieri-Ramirez, Matthew Wallard, Simon Pilgrim, Dylan R. Edwards

5. Identification of Protease Substrates by Mass Spectrometry Approaches-1
Mari Enoksson, Wenhong Zhu, Guy S. Salvesen

6. Identification of Protease Substrates by Mass Spectrometry Approaches-2
Anna Prudova, Ulrich Keller, Christopher M. Overall

7. Activity-Based Imaging and Biochemical Profiling Tools for Analysis of the Cancer Degradome
Vincent Dive, Margot G. Paulick, J. Oliver McIntyre, Lynn M. Matrisian, Matthew Bogyo

8. Images of Cleavage: Tumor Proteases in Action
Kamiar Moin, Mansoureh Sameni, Christopher Jedeszko, Quanwen Li, Mary B. Olive, Raymond R. Mattingly, Bonnie F. Sloane

II. Insights into Protease Function

9. Proteolytic Pathways: Intersecting Cascades in Cancer Development
Nesrine I. Affara, Lisa M. Coussens

10. Physiological Functions of Plasminogen Activation: Effects of Gene Deficiencies in Humans and Mice
Thomas H. Bugge

11. The Plasminogen Activation System in Tissue Remodeling and Cancer Invasion
Kasper Almholt, Anna Juncker-Jensen, Kirsty Anne Green, Helene Solberg, Leif Røge Lund, John Rømer

12. The Urokinase Plasminogen Activator Receptor as a Target for Cancer Therapy
Silvia D’Alessio, Francesco Blasi

13. The Endocytic Collagen Receptor, uPARAP/Endo180, in Cancer Invasion and Tissue Remodeling
Thore Hillig, Lars H. Engelholm, Niels Behrendt

14. Physiological and Pathological Functions of Type II Transmembrane Serine Proteases: Lessons from Transgenic Mouse Models and Human Disease-Associated Mutations
Karin List, Thomas H. Bugge

15. Roles of Cysteine Proteases in Tumor Progression: Analysis of Cysteine Cathepsin Knockout Mice in Cancer Models
Thomas Reinheckel, Vasilena Gocheva, Christoph Peters, Johanna A. Joyce

16. In Vitro and In Vivo Models of Angiogenesis to Dissect MMP Functions
Sarah Berndt, Françoise Bruyère, Maud Jost, Agnès Noël

17. The Surface Transplantation Model to Study the Tumor–Host Interface
Maud Jost, Silvia Vosseler, Silvia Blacher, Norbert E. Fusenig, Margareta M. Mueller, Agnès Noël

18. Unravelling the Roles of Proteinases in Cell Migration In Vitro and In Vivo
Jelena Gavrilovic, Xanthe Scott

19. New Insights into MMP function in Adipogenesis
Kumari L. Andarawewa, Marie-Christine Rio

20. TIMPs: Extracellular Modifiers in Cancer Development
Aditya Murthy, William Cruz-Munoz, Rama Khokha

III. The Interface Between Proteolysis and Cell Signalling

21. Invadopodia: Interface for Invasion
Susette C. Mueller, Vira V. Artym, Thomas Kelly

22. uPAR and Proteases in Mobilization of Hematopoietic Stem Cells
Pia Ragno, Francesco Blasi

23. The Urokinase Receptor and Integrins Constitute a Cell Migration Signalosome
Bernard Degryse

24. Measuring uPAR Dynamics in Live Cells
Moreno Zamai, Gabriele Malengo, Valeria R. Caiolfa

25. Janus-Faced Effects of Broad-Spectrum and Specific MMP Inhibition on Metastasis
Charlotte Kopitz, Achim Krüger

26. Cytokine Substrates: MMP Regulation of Inflammatory Signaling Molecules
Jennifer H. Cox, Christopher M. Overall

27. Matrix Metalloproteinases as Key Regulators of Tumor–Bone Interaction
Conor C. Lynch, Lynn M. Matrisian

IV. The Degradome as Source of Cancer Diagnostic and Markers

28. The Plasminogen Activation System as a Source of Prognostic Markers in Cancer
Ib Jarle Christensen, Helle Pappot, Gunilla Høyer-Hansen

29. Cysteine Cathepsins and Cystatins as Cancer Biomarkers
Tamara T. Lah, Nataša Obermajer, María Beatriz Durán Alonso, Janko Kos

30. Novel Degradome Markers in Breast Cancer
Caroline J. Pennington, Simon Pilgrim, Paul N. Span, Fred C. Sweep, Dylan R. Edwards

31. Meta-Analysis of Gene Expression Microarray Data: Degradome Genes in Healthy and Cancer Tissues
Kristiina Iljin, Sami Kilpinen, Johanna Ivaska, Olli Kallioniemi

32. Degradome Gene Polymorphisms
Ross Laxton, Shu Ye

33. TIMP-1 as a Prognostic Marker in Colorectal Cancer
Camilla Frederiksen, Anne Fog Lomholt, Hans Jørgen Nielsen, Nils Brünner

V. Novel Therapeutic Strategies

34. Structure and Inhibition of the Urokinase-Type Plasminogen Activator Receptor
Benedikte Jacobsen, Magnus Kjaergaard, Henrik Gårdsvoll, Michael Ploug

35. Engineered Antagonists of uPA and PAI-1
M. Patrizia Stoppelli, Lisbeth M. Andersen, Giuseppina Votta, Peter A. Andreasen

36. MMP Inhibitor Clinical Trials – The Past, Present, and Future
Barbara Fingleton

37. Tailoring TIMPs for Selective Metalloproteinase Inhibition
Hideaki Nagase, Gillian Murphy

38. Third-Generation MMP Inhibitors: Recent Advances in the Development of Highly Selective Inhibitors
Athanasios Yiotakis, Vincent Dive

39. Protease-Activated Delivery and Imaging Systems
Gregg B. Fields

40. Development of Tumour-Selective and Endoprotease-Activated Anticancer Therapeutics
Jason H. Gill, Paul M. Loadman

41. Targeting Degradome Genes via Engineered Viral Vectors
Risto Ala-aho, Andrew H. Baker, Veli-Matti Kähäri

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Keywords: TECHNOLOGY & ENGINEERING / Biomedical TEC059000