3D cell-based biosensors in drug discovery programs : microtissue engineering for high throughput screening

Title:

Personal Author:

Kisaalita, William Ssempa, 1953-

Publication Information:

Boca Raton : CRC Press, c2010

Physical Description:

xvii, 386 pages. : illustrations. ; 25 cm.

ISBN:

9781420073492

Abstract:

"This book is based upon cutting-edge research conducted in the authors lab (Cellular Bioengineering), which over the past decade has developed a number of sophisticated techniques to facilitate use of 3D cell based assays or biosensors. This book uses data from peer-reviewed publications to conclusively justify use of 3D cell cultures in cell-based biosensors (assays) for (HTS). The majority of assays performed in accelerated drug discovery processes are biochemical in nature, but there is a growing demand for live cell-based assays. Unlike biochemical ones, cellular assays are functional approximations of in vivo biological conditions and can provide more biologically relevant information"--Provided by publisher.

Subject Term:

Pharmaceutical biotechnology

Biosensors

High throughput screening (Drug development)

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Library	Item Barcode	Call Number	Material Type	Item Category 1	Status
Searching... PSZ JB	30000010273785	RS380 K537 2010	Open Access Book	Book	Searching... Unknown

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Summary

Advances in genomics and combinatorial chemistry during the past two decades inspired innovative technologies and changes in the discovery and pre-clinical development paradigm with the goal of accelerating the process of bringing therapeutic drugs to market. Written by William Kisaalita, one of the foremost experts in this field, 3D Cell-Based Biosensors in Drug Discovery Programs: Microtissue Engineering for High Throughput Screening provides the latest information -- from theory to practice -- on challenges and opportunities for incorporating 3D cell-based biosensors or assays in drug discovery programs.

The book supplies a historical perspective and defines the problem 3D cultures can solve. It also discusses how genomics and combinatorial chemistry have changed the way drug are discovered and presents data from the literature to underscore the less-than-desirable pharmaceutical industry performance under the new paradigm. The author uses results from his lab and those of other investigators to show how 3D micro environments create cell culture models that more closely reflect normal in vivo-like cell morphology and function. He makes a case for validated biomarkers for three-dimensionality in vitro and discusses the advantages and disadvantages of promising tools in the search of these biomarkers. The book concludes with case studies of drugs that were abandoned late in the discovery process, which would have been discarded early if tested with 3D cultures.

Dr. Kisaalita presents evidence in support of embracing 3D cell-based systems for widespread use in drug discovery programs. He goes to the root of the issue, establishing the 3D cell-based biosensor physiological relevance by comparing 2D and 3D culture from genomic to functional levels. He then assembles the bioengineering principles behind successful 3D cell-based biosensor systems. Kisaalita also addresses the challenges and opportunities for incorporating 3D cell-based biosensors or cultures in current discovery and pre-clinical development programs. This book makes the case for widespread adoption of 3D cell-based systems, rendering their 2D counterparts, in the words of Dr. Kisaalita "quaint, if not archaic" in the near future.

Author Notes

Preface	p. xv
Author	p. xvii
Part I Introduction
Chapter 1 Biosensors and Bioassays	p. 3
1.1 Conventional Biosensors	p. 3
1.2 Conventional Biosensor Applications	p. 8
1.2.1 Bioprocess Monitoring and Control	p. 9
1.2.2 Food Quality Control	p. 9
1.2.3 Environmental Monitoring	p. 9
1.2.4 Military Biodefense Applications	p. 12
1.2.5 Clinical Diagnostics	p. 13
1.3 Cell-Based Biosensors versus Cell-Based Assays (Bioassays)	p. 13
1.4 3D Cultures	p. 15
1.4.1 Two-Dimensional (2D) Culture Systems	p. 15
1.4.2 3D Culture Systems	p. 18
1.4.3 Tissue Engineering versus Microtissue Engineering	p. 18
1.5 Concluding Remarks	p. 19
References	p. 19
Chapter 2 Target-Driven Drug Discovery	p. 23
2.1 Drug Discovery and Development	p. 23
2.1.1 Target	p. 23
2.1.2 Hit	p. 23
2.1.3 Lead	p. 24
2.1.4 Candidate	p. 24
2.1.5 Investigational New Drug (IND) Application	p. 24
2.1.6 Drug or Product	p. 24
2.2 The Taxol (Paclitaxel) Discovery Case	p. 25
2.3 The Gleevec (Imatinib Mesylate) Discovery Case	p. 35
2.4 Target-Driven Drug Discovery Paradigm	p. 43
2.4.1 Genomics and Proteomics	p. 44
2.4.2 Combinatorial Chemistry	p. 46
2.4.3 HTS/uHTS	p. 47
2.5 The New Discovery Paradigm Promise	p. 47
2.6 Concluding Remarks	p. 49
References	p. 51
Part II 3D versus 2D Cultures
Chapter 3 Comparative Transcriptional Profiling and Proteomics	p. 57
3.1 Transcriptional Profiling Studies	p. 57
3.2 Comparative GO Annotation Analysis	p. 60
3.3 Proteomics Studies	p. 65
3.4 Concluding Remarks	p. 67
References	p. 74
Chapter 4 Comparative Structure and Function	p. 77
4.1 Complex Physiological Relevance	p. 77
4.2 Cardiomyocyte Contractility	p. 78
4.2.1 Cells and Scaffold	p. 78
4.2.2 Comparative Structure	p. 78
4.2.3 Comparative Function	p. 79
4.2.4 HTS Application Feasibility	p. 80
4.3 Liver Cell Bile Canaliculi In Vitro	p. 82
4.3.1 Cells and Scaffold	p. 82
4.3.2 Comparative Structure and Function	p. 83
4.3.3 HTS Application Feasibility	p. 84
4.4 Nerve Cell Voltage-Gated Calcium Signaling	p. 84
4.4.1 Cells and Scaffold	p. 84
4.4.2 Comparative Structure	p. 86
4.4.3 Comparative Function	p. 87
4.4.4 HTS Application Feasibility	p. 89
4.5 Concluding Remarks	p. 89
References	p. 90
Part III Emerging Design Principles
Chapter 5 Chemical Microenvironmental Factors	p. 97
5.1 Cell Adhesion Molecules	p. 97
5.1.1 Cadherins	p. 97
5.1.2 Selectins	p. 99
5.1.3 The Integrin Superfamily	p. 101
5.1.4 The Ig-Domain-Containing Superfamily of CAMs	p. 103
5.2 Short-Range Chemistry	p. 103
5.2.1 ECM Composition	p. 104
5.2.2 Substrate Surface Chemistry	p. 108
5.3 Long-Range Chemistry	p. 110
5.3.1 Cytokines, Chemokines, Hormones, and Growth Factors	p. 111
5.3.2 Matrix Metalloproteinases (MMPs)	p. 112
5.4 Concluding Remarks	p. 112
References	p. 115
Chapter 6 Spatial and Temporal Microenvironmental Factors	p. 121
6.1 Nano- and Microstructured Surfaces	p. 122
6.2 Scaffolds	p. 122
6.3 Nano and Scaffold-Combined Structures	p. 148
6.4 Temporal Factor	p. 148
6.5 Concluding Remarks	p. 153
References	p. 160
Chapter 7 Material Physical Property and Force Microenvironmental Factors	p. 169
7.1 Basics	p. 169
7.1.1 Young's Modulus, Stiffness, and Rigidity	p. 169
7.1.2 Shear Modulus or Modulus of Rigidity	p. 170
7.1.3 Material Physical Properties Characterization	p. 171
7.1.4 Contractile Force Generation in Cells	p. 177
7.1.5 Force and Geometry Sensing	p. 179
7.2 Stiffness-Dependent Responses	p. 180
7.2.1 Biological and Nonbiological Materials' Stiffness	p. 180
7.2.2 Stiffness-Dependent Morphology and Adhesion	p. 182
7.2.3 Stiffness-Dependent Migration	p. 183
7.2.4 Stiffness-Dependent Growth and Differentiation	p. 185
7.2.5 Substrate Stiffness-Dependent Cell's Internal Stiffness	p. 187
7.3 Force-Dependent Responses	p. 189
7.4 Concluding Remarks	p. 193
References	p. 198
Chapter 8 Proteomics as a Promising Tool in the Search for 3D Biomarkers	p. 207
8.1 Why Search for Three-Dimensionality Biomarkers?	p. 207
8.2 Cellular Adhesions	p. 209
8.3 Signaling Pathways	p. 212
8.4 Overview of Proteomics Techniques	p. 213
8.4.1 Protein Separation by Two-Dimensional Polyacrylamide Gel Electrophoresis (2DE)	p. 213
8.4.2 Peptide Detection	p. 214
8.4.3 Protein Identification	p. 214
8.5 Study Design and Methods	p. 215
8.5.1 Addressing Low-Abundance and Poor Solubility Proteins	p. 215
8.5.2 Biomarker Validation	p. 216
8.6 Concluding Remarks	p. 217
References	p. 217
Chapter 9 Readout Present and Near Future	p. 221
9.1 Readout Present and Near Future	p. 221
9.2 Fluorescence-Based Readouts	p. 224
9.2.1 Jablonski Diagram and Fluorescence Basics	p. 224
9.2.2 Fluorescence Readout Configurations	p. 225
9.3 Bioluminescence-Based Readouts	p. 230
9.4 Label-Free Biosensor Readouts	p. 235
9.4.1 Impedance	p. 235
9.4.2 Surface Plasmon Resonance	p. 242
9.5 Concluding Remarks	p. 245
References	p. 246
Chapter 10 Ready-to-Use Commercial 3D Plates	p. 253
10.1 Introduction	p. 253
10.2 Algimatrix™	p. 254
10.2.1 Fabrication	p. 254
10.2.2 Complex Physiological Relevance	p. 255
10.2.3 Unique Features	p. 256
10.3 Extracel™	p. 257
10.3.1 Synthesis	p. 257
10.3.2 Complex Physiological Relevance	p. 257
10.3.3 Unique Features	p. 257
10.4 Ultra-Web™	p. 259
10.4.1 Fabrication	p. 260
10.4.2 Complex Physiological Relevance	p. 260
10.4.3 Unique Features	p. 261
10.5 Market Opportunities	p. 262
10.5.1 The Opportunity	p. 262
10.5.2 Potential Customers	p. 262
10.5.3 Market Size	p. 263
10.5.4 Market Size Estimation	p. 263
10.6 Concluding Remarks	p. 264
References	p. 265
Part IV Technology Deployment Challenges and Opportunities
Chapter 11 Challenges to Adopting 3D Cultures in HTS Programs	p. 269
11.1 Typical HTS Laboratory and Assay Configurations	p. 269
11.2 Just-in-Time Reagents Provision Model	p. 274
11.3 Limited Value-Addition from 3D Culture Physiological Relevance: Transepithelium Drug Transport and Induction of Drug Metabolizing Enzyme Cases	p. 276
11.3.1 Transepithelium Drug Transport: Caco-2 Assay	p. 276
11.3.2 Induction of Drug Metabolizing Enzymes: Hepatocyte Assays	p. 283
11.4 Paucity of Conclusive Support of 3D Culture Superiority	p. 283
References	p. 285
Chapter 12 Cases for 3D Cultures in Drug Discovery	p. 289
12.1 Three Cases	p. 289
12.2 The ß1-Integrin Monoclonal Antibody Case	p. 289
12.2.1 Integrins	p. 289
12.2.2 Monoclonal Antibodies	p. 290
12.2.3 Experimental System: Breast Cancer Cells in Matrigel	p. 293
12.2.4 Treatment with ß1-Integrin Inhibitory Antibody Reduced Malignancy in In Vitro-3D and In Vivo, but Not in In Vitro-2D Systems	p. 293
12.3 The Matrix Metalloproteinase Inhibitors Case	p. 294
12.3.1 Extracellular Matrix Metalloproteinases (MMPs)	p. 294
12.3.2 MMP Inhibitors (MMPIs)	p. 295
12.3.3 Experimental System: Fibrosarcoma Cells in Collagen Gels	p. 295
12.3.4 Treatment with Pericellular Proteolysis Inhibitors in 3D Cultures and In Vivo Did Not Prevent Cell Migration or Metastasis	p. 296
12.4 Resistance to the Chemotherapeutic Agents Case	p. 297
12.4.1 Experimental System: Multicellular Tumor Spheroid (MCTS)	p. 297
12.4.2 MCTS More Accurately Approximate In Vivo Resistance to Chemotherapeutic Agents	p. 298
12.5 Concluding Remarks	p. 300
References	p. 301
Chapter 13 Ideal Case Study Design	p. 307
13.1 Rationale for the Case Study	p. 307
13.2 Why Hepatotoxicity?	p. 308
13.2.1 Morphology of the Liver	p. 308
13.2.2 What Is Hepatotoxicity?	p. 308
13.3 Hepatotoxicity and hESC-Derived Hepatocyte-Like Cells	p. 310
13.3.1 Two Reasons Why IADRs Have Attracted Proposed Studies	p. 310
13.3.2 IADRs and Mitochondrial Inner Transmembrane Potential (¿¿ m )	p. 314
13.4 Study Design and Methods	p. 317
13.4.1 Experimental Design and Rationale	p. 317
13.4.2 Cell Culture and Drug Exposure	p. 318
13.4.3 Expression of Drug-Metabolizing Enzymes	p. 318
13.4.4 Alanine Aminotransferase (ATL) Activity Assay	p. 318
13.4.5 Mitochondrial Membrane Potential (¿¿ m ) Measurement	p. 318
13.5 Analysis and Expected Results	p. 319
13.5.1 Quality Assessment of HTS Assays	p. 319
13.5.2 Expected Results	p. 319
13.5.3 Potential Pitfalls	p. 320
References	p. 320
Appendix A Patents for 3D Scaffolds	p. 323
References	p. 328
Appendix B Current Drug Targets	p. 331
Appendix C Popular Cell Lines in Drug Discovery	p. 357
C1 HEK 293	p. 357
C1.1 Background	p. 357
C1.2 Morphology and Ploidy	p. 358
C2 CHO	p. 358
C2.1 Background	p. 358
C2.2 Morphology and Ploidy	p. 358
C3 HeLa	p. 358
C3.1 Background	p. 358
C3.2 Morphology and Ploidy	p. 359
C4 HepG2	p. 359
C4.1 Background	p. 359
C4.2 Morphology and Ploidy	p. 360
C5 U2OS	p. 360
C5.1 Background	p. 360
C5.2 Morphology and Ploidy	p. 360
C6 COS-7/CV-1	p. 360
C6.1 Background	p. 360
C6.2 Morphology and Ploidy	p. 361
References	p. 361
Appendix D Stem Cells in Drug Discovery	p. 363
References	p. 368
Index	p. 373
Company Index	p. 385

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Author Notes

Table of Contents