The potentials of MS‐based subproteomic approaches in medical science: The case of lysosomes and breast cancer

  I. Introduction 00  II. Functions and Biogenesis of the Lysosome 00 III. Lysosomes and Breast Cancer 00A.  Lysosomal Hydrolases 00    1.  Roles of the Lysosomal Enzymes in the Development of Breast Cancer 00a.  ECM Degradation 00b.  Angiogenesis 00c.  Cell Proliferation and Apoptosis: Specific Roles of CatD 00d.  Lysosomal Hydrolases at the Site of Metastasis 00    2.  Modifications of the Expression, Targeting, and Glycosylation Processing of Lysosomal Enzymes 00a.  Overexpression of Lysosomal Hydrolases 00b.  Altered Trafficking of Lysosomal Hydrolases 00c.  Mannose‐6‐Phosphorylation 00    3.  Lysosomal Enzymes as Breast Cancer Biomarkers 00a.  The Aspartic Protease, CatD 00b.  The Cysteine Proteases, CatB and CatL 00c.  Other Lysosomal Soluble Proteins 00B.  M6P/IGFIIR and Breast Cancer 00    1.  M6P/IGFIIR Involvment in Cancer: Clinical and Experimental Evidence 00    2.  Biological and Physiological Mechanisms That Lead to Tumor Progression and Metastasis, Related to M6P/IGFIIR 00C.  Lysosomal Membrane Proteins 00    1.  LAMP‐1 and LAMP‐2 00    2.  The Tetraspanin, CD63 00D.  Conclusions 00 IV. Subproteomics: The Example of the Lysosome, Phagolysosome, and Lysosome‐Related Organelles 00A.  Fractionation and Starting Material 00B.  Analytical Strategies to Identify Proteins From Lysosomes and Lysosome‐Related Organelles 00C.  Checking the Localization of Lysosomal Proteins 00D.  How to Decipher the Function of Lysosomal Proteins? 00  V. Lysosomes and Breast Cancer: What are the Challenges for MS‐Based Proteomic Approaches? 00A.  Starting Material: The Breast Cancer Cells 00    1.  Cell Lines Versus Tumor Samples: General Statements 00    2.  The Use of Breast Cancer Cells to Study the Lysosome or Lysosome‐Related Compartment 00a.  Breast Cancer Cell Lines 00b.  Microdissected cells 00B.  MS‐Based Methods for a Better Understanding of Lysosomes in the Context of Breast Cancer 00    1.  How to Quantitate the Differential Expression of Lysosomal Proteins in the Case of Breast Cancer? 00    2.  PTMs of Lysosomal Proteins: How Can They be Monitored? 00    3.  Identification of Membrane Proteins to Study Breast Cancer 00 VI. Conclusions 00 Acknowledgments 00 Abbreviations 00 References 00Because of the great number of women who are diagnosed with breast cancer each year, and though this disease presents the lowest mortality rate among cancers, breast cancer remains a major public health problem. As for any cancer, the tumorigenic and metastatic processes are still hardly understood, and the biochemical markers that allow either a precise monitoring of the disease or the classification of the numerous forms of breast cancer remain too scarce. Therefore, great hopes are put on the development of high‐throughput genomic and proteomic technologies. Such comprehensive techniques should help in understanding the processes and in defining steps of the disease by depicting specific genes or protein profiles. Because techniques dedicated to the current proteomic challenges are continuously improving, the probability of the discovery of new potential protein biomarkers is rapidly increasing. In addition, the identification of such markers should be eased by lowering the sample complexity; e.g., by sample fractionation, either according to specific physico‐chemical properties of the proteins, or by focusing on definite subcellular compartments. In particular, proteins of the lysosomal compartment have been shown to be prone to alterations in their localization, expression, or post‐translational modifications (PTMs) during the cancer process. Some of them, such as the aspartic protease cathepsin D (CatD), have even been proven as participating actively in the disease progression. The present review aims at giving an overview of the implication of the lysosome in breast cancer, and at showing how subproteomics and the constantly refining MS‐based proteomic techniques may help in making breast cancer research progress, and thus, hopefully, in improving disease treatment. © 2004 Wiley Periodicals, Inc., Mass Spec Rev