Antigen Retrieval Immunohistochemistry Based Research and Diagnostics

Shan-Rong Shi, MD, is professor of clinical pathology at the Keck School of Medicine of the University of Southern California. He is the Associate Editor of The Journal of Histochemistry and cytochemistry, he is on the Editoral Board of Applied Immunohistochemistry and Molecular Morphology and is also on the Overseas Editorial Board of the Chinese Journal of Pathology. Dr. Shi is the ineventor of the antigen retrieval (AR) technique. Clive R. Taylor, MD, PhD, is Senior Associate Dean, Professor and Chairman of Pathology at the Keck School of Medicine. Dr. Taylor is Editor in Chief of Applied Immunohistochemistry and Molecular Morphology. Dr. Taylor is a world renowned expert in immunohistochemistry and clinical pathology.

Preface ix

Contributors xv

Part I Recent Advances in Antigen Retrieval Techniques and Its Application 1

1 Standardization of Antigen Retrieval Techniques Based on the Test Battery Approach 3
Shan-Rong Shi and Clive R. Taylor

2 Extended Application of Antigen Retrieval Technique in Immunohistochemistry and in Situ
Hybridization 25
Shan-Rong Shi and Clive R. Taylor

3 Extraction of Dna/rna From Formalin-fixed, Paraffin-embedded Tissue Based on the Antigen Retrieval Principle 47
Shan-Rong Shi and Clive R. Taylor

Part II Standardization of Immunohistochemistry 73

4 Key Issues and Strategies of Standardization For Quantifiable Immunohistochemistry 75
Shan-Rong Shi, Kevin A. Roth, and Clive R. Taylor

5 Standardization of Immunohistochemistry Based on Antigen Retrieval Technique 87
Shan-Rong Shi and Clive R. Taylor

6 Standard Reference Material: Cell Line Development and Use of Reference Cell Lines as Standards for External Quality Assurance of Her2 Ihc and Ish Testing 101
Bharat Jasani, Vicky Reid, Colin Tristram, Jeremy Walker, Paul Scorer, Michael Morgan, John Bartlett, Merdol Ibrahim, and Keith Miller

7 Peptides as Immunohistochemistry Controls 123
Steven A. Bogen and Seshi R. Sompuram

8 Standard Reference Material: Protein- Embedding Technique and Design of Bar Code 141
Shan-Rong Shi, Jiang Gu, and Clive R. Taylor

9 the Pros and Cons of Automation for Immunohistochemistry From the Prospective Of the Pathology Laboratory 151
David G. Hicks and Loralee McMahon

10 Image Analysis in Immunohistochemistry 165
Alton D. Floyd

Part III Tissue/cell Sample Preparation 187

11 Tissue Cell Sample Preparation: Lessons From the Antigen Retrieval Technique 189
Shan-Rong Shi and Clive R. Taylor

12 Mechanisms of Action and Proper Use of Common Fixatives 195
Richard W. Dapson

13 Cell Sample Preparation for Clinical Cytopathology: Current Status and Future Development 219
Yan Shi and Patricia G. Wasserman

14 Design of a Tissue Surrogate to Examine Accuracy of Proteomic Analysis 235
Carol B. Fowler, Jeffrey T. Mason, and Timothy J. O’leary

Part IV Molecular Mechanism of Antigen Retrieval Technique 251

15 Study of Formalin Fixation and Heat-induced Antigen Retrieval 253
Jeffrey T. Mason, Carol B. Fowler, and Timothy J. O’leary

16 a Linear Epitopes Model of Antigen Retrieval 287
Steven A. Bogen and Seshi R. Sompuram

17 Ph Or Ionic Strength of Antigen Retrieval Solution: a Potential Role for Refolding During Heat Treatment 303
Shuji Yamashita

18 Commentary: Future Directions 323
Timothy J. O’Leary, Carol B. Fowler, David L. Evers, Robert E. Cunningham, and Jeffrey T. Mason

Part V Proteomic Analysis of Protein Extracted From Tissue/cells 333

19 Techniques of Protein Extraction From Ffpe Tissue/cells for Mass Spectrometry 335
Carol B. Fowler, Timothy J. O’Leary, and Jeffrey T. Mason

20 Application of Shotgun Proteomics to Formalin-fixed and Paraffin-embedded Tissues 347
Brian M. Balgley

21 Visualizing Protein Maps in Tissue 369
Masahiro Mukai and Mitsutoshi Setou

22 Symbiosis of Immunohistochemistry and Proteomics: Marching to a New Era 391
Shan-Rong Shi, Brian M. Balgley, and Clive R. Taylor

Appendix Related Laboratory Protocols 399

Index 413