Design of Nanostructures for Theranostics Applications

By Alexandru Mihai Grumezescu

Design of Nanostructures for Theranostics Applications focuses on the theranostics applications of nanostructures. In particular, multifunctional nanoparticles for diagnostics and treatment of different diseases, including those relating to the blood-brain barrier, are discussed in detail. Chapters explore different type of nanostructures, covering design, fabrication, functionalization and optimization, helping readers obtain the desired properties. Written by a diverse range of international academics, this book is a valuable reference resource for those working in both nanoscience and the pharmaceutical industry.

• Explores how the design of a range of nanomaterials make them effective theranostic agents, including multifunctional core-shell nanostructures, mesoporous silica nanoparticles, and quantum dots
• Shows how nanomaterials are used effectively for a range of diseases, including breast cancer, prostate cancer and neurological disorders
• Assesses the pros and cons of using different nanomaterials for different types of treatment

• Language: English
• Publisher: Elsevier Science
• Release date: Nov 30, 2017
• ISBN: 9780128136706

Book preview

Design of Nanostructures for Theranostics Applications

Edited by

Alexandru Mihai Grumezescu

Faculty of Applied Chemistry and Materials Science, University Politehnica of Bucharest, Romania

Table of Contents

Cover image

Title page

Copyright

List of Contributors

Series Preface: Pharmaceutical Nanotechnology

Preface

Chapter 1. Novel diagnostic techniques: Genomic, proteomic and systems biology approaches

Abstract

1.1 Introduction

1.2 Molecular Diagnostics Era

1.3 Molecular Technologies for Cancer Diagnostics

1.4 Cancer Theranostics

1.5 Nanotechnologic Approaches in Cancer Diagnostics

1.6 Clinical Applications

1.7 Future Aspects of Molecular Diagnostic Tools

1.8 Conclusion

References

Chapter 2. Nanotheranostics and theranostic nanomedicine for diseases and cancer treatment

Abstract

2.1 Introduction

2.2 Theranostic Nanomedicine

2.3 Nanotheranostics Drug Targeting

2.4 Different Types of Nanotheranostics

2.5 Role of Theranostic Nanomedicine in Cancer Treatment

2.6 Nanotheranostics for Photothermal and Photodynamic Cancer Therapy

2.7 Theranostic Applications of Magnetic Nanoparticles in Cancer

2.8 Magnetic Hyperthermia

2.9 Engineered Mammalian Cell-Based Theranostic Agents for Cancer Therapy

2.10 Imaging Drug Delivery in Cancer Diagnostics

2.11 Theranostic Nanomedicine in Cardiovascular Diseases

2.12 Theranostics for Treatment of Diseases of the Central Nervous System

2.13 Conclusions

References

Further Reading

Chapter 3. A novel approach for drug targeting: Core-shell type lipid-polymer hybrid nanocarriers

Abstract

3.1 Introduction

3.2 Structure of Core-Shell Type Lipid-Polymer Hybrid Systems

3.3 Major Advantages

3.4 Preparation Methods

3.5 Physicochemical Characteristics

3.6 Applications as Drug Delivery

3.7 Conclusion

References

Further Reading

Chapter 4. Multifunctional core–shell polymeric and hybrid nanoparticles as anticancer nanomedicines

Abstract

4.1 Core–Shell Nanoparticles as Carriers for Tumor Targeting: Evolution and Challenges

4.2 Common Types of Core–Shell Nanoparticles and Their Biomedical Application

4.3 Hybrid Metal-Organic Framework Nanoparticles

4.4 Conclusion: Translation From Research to Implementation

Acknowledgments

References

Chapter 5. Silver-, gold-, and iron-based metallic nanoparticles: Biomedical applications as theranostic agents for cancer

Abstract

5.1 Silver-, Gold- and Iron-Based Nanoparticles in the Anticancer Field of Research: Overview

5.2 Classification and Technological Approaches

5.3 Gold Nanoparticles

5.4 Silver Nanoparticles

5.5 Iron Nanoparticles

5.6 Conclusions and Future Perspectives

Acknowledgment

References

Further Reading

Chapter 6. Functional stimuli-responsive polymeric network nanogels as cargo systems for targeted drug delivery and gene delivery in cancer cells

Abstract

6.1 Introduction

6.2 Stimuli-Responsive Nanogels as Targeted Drug Delivery in Cancer Cells

6.3 Nanogels as Gene Delivery in Cancer Cells

6.4 Conclusions and Future Outlook

Acknowledgments

References

Chapter 7. Dendrimer-drug conjugates: Synthesis strategies, stability and application in anticancer drug delivery

Abstract

7.1 Dendrimer-Based Drug Delivery Strategies

7.2 Advantages of Dendrimer-Drug Conjugates

7.3 Strategies for Synthesis of Dendrimer-Drug Conjugates

7.4 Stability of Dendrimer-Drug Conjugates in the Biological System

7.5 Efficacy of Dendrimer-Drug Conjugate Compared to Native Drug

7.6 Drug-Dendrimer Conjugates-Mediated Solubility Enhancement of Anticancer Drugs

7.7 Drug-Dendrimer Conjugates-Mediated Altered Pharmacokinetics of Anticancer Drugs

7.8 Targeted Drug-Dendrimer Conjugates

7.9 Conclusions

Acknowledgements

References

Chapter 8. Liposomes and micelles as nanocarriers for diagnostic and imaging purposes

Abstract

8.1 Introduction

8.2 Future Perspectives and Conclusions

References

Chapter 9. Small RNA-mediated prevention, diagnosis and therapies of cancer

Abstract

9.1 Introduction

9.2 Biology of Oligonucleotide-Mediated Gene Silencing

9.3 Applications of RNA Interference in Cancer

9.4 Chemical and Structural Modifications of Small RNA-Based Therapeutics

9.5 Delivery of Therapeutic Small RNAs

9.6 Emerging Small RNA-Based Technologies in Cancer Biology

9.7 Conclusions and Perspectives

References

Chapter 10. Mesoporous silica nanoparticles as drug delivery systems against melanoma

Abstract

10.1 Introduction

10.2 Physicochemical Properties

10.3 Biocompatibility and Toxicity Assessment

10.4 Mesoporous Silica Nanoparticles for Controlled Release

10.5 Synthesis Methods

10.6 Characterization Methods of Mesoporous Carriers

10.7 In Vitro and In Vivo Studies

10.8 Impact of Shape at the Cellular Level

10.9 Cancer Therapy Based on Mesoporous Silica Nanoparticles

10.10 Melanoma, a Potential Target for Mesoporous Silica Nanoparticles

10.11 Summary

Acknowledgments

References

Chapter 11. Current approaches in breast cancer targeting pharmaceuticals

Abstract

11.1 Introduction

11.2 The Molecular Pathology of Breast Cancer

11.3 New Approaches in Cancer Pharmaceuticals

11.4 Current View on Trastuzumab Therapy

11.5 Conclusions

References

Further Reading

Chapter 12. Conventional and current imaging techniques in cancer research and clinics

Abstract

12.1 Importance of Imaging in Oncology

12.2 Imaging Approaches

12.3 Novel Technologies

12.4 Future Directions

12.5 Conclusion

References

Chapter 13. Role of nanoparticles in bioimaging, diagnosis and treatment of cancer disorder

Abstract

13.1 Introduction

13.2 Biocompatibility of Nanoparticles With Biological Components

13.3 Biomedical Applications of Nanoparticles

13.4 Cancer-Specific Action of Nanoparticles

13.5 Limitations and Challenges of Nanoparticle Action in Cancer Treatment

13.6 Troubleshooting of Nanoparticle Limitations for Cancer Treatment

13.7 Possible Outcome of Nanoparticle Application in Cancer Treatment

13.8 Future Perspectives

Abbreviations

Acknowledgements

References

Chapter 14. Synthetic microbial ecology and nanotechnology for the production of Taxol and its precursors: A step towards sustainable production of cancer therapeutics

Abstract

14.1 Introduction

14.2 Origin of the Synthetic Microbial Consortia

14.3 Taxus: A Novel Plant With Beneficial Microbial Diversity

14.4 Pertinence of Monocultures for Synthetic Consortia

14.5 Bioprocess Engineering and Nanotechnology in Production of Therapeutic Compounds

14.6 Nanobiochips and Nanodevices: A Fair Choice to Get the Higher Production of Taxol

14.7 Conclusions

References

Further Reading

Chapter 15. Trastuzumab drug delivery systems for magnetic resonance imaging detection

Abstract

15.1 Introduction

15.2 Why are Certain Drugs More Efficient than Others?

15.3 How to Model a Tumor?

15.4 Methodology of Magnetic Resonance Spectroscopy, Magnetic Resonance Imaging and Relaxation Techniques

15.5 Breast Cancer Treatments With Trastuzumab During the Years 1998–2016

15.6 Current Trastuzumab Drug Delivery Systems for Magnetic Resonance Imaging

15.7 Conclusion

References

Further Reading

Chapter 16. Recent advancement in cancer treatment

Abstract

16.1 Introduction

16.2 Recent Advances in Cancer Immunotherapy

16.3 Recent Advances in Surgery

16.4 Recent Advances in Robotic Radiotherapy

16.5 Advances in Gene Therapy

16.6 Advances in Hormonal Therapy

16.7 Advances in Photothermal Therapy

16.8 Conclusion

References

Index

Copyright

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List of Contributors

David Aebisher

Shorter University, Rome, GA, United States

University of Rzeszów, Rzeszów, Poland

Abdullah Al Hasan,     Southeast University, Dhaka, Bangladesh

Florina Andrica,     University of Medicine and Pharmacy Victor Babes Timisoara, Eftimie Murgu, Romania

S. Antunes,     University of Coimbra, Coimbra, Portugal

Nezahat Pinar Barkan,     Hacettepe University, Ankara, Turkey

Dorota Bartusik

University of Rzeszów, Rzeszów, Poland

Southern Polytechnic State University, Marietta, GA, United States

Dorina Coricovac,     University of Medicine and Pharmacy Victor Babes Timisoara, Eftimie Murgu, Romania

Corina Danciu,     University of Medicine and Pharmacy Victor Babes Timisoara, Eftimie Murgu, Romania

Cristina Dehelean,     University of Medicine and Pharmacy Victor Babes Timisoara, Eftimie Murgu, Romania

Simona Dimchevska,     SS Cyril and Methodius University, Skopje, Macedonia

Catalano Enrico,     University of Oslo (UiO), Oslo, Norway

Nikola Geskovski,     SS Cyril and Methodius University, Skopje, Macedonia

Katerina Goracinova,     SS Cyril and Methodius University, Skopje, Macedonia

Ruxandra Gref,     Université Paris-Sud, Orsay, France

Mehmet Gumustas,     Ankara University, Ankara, Turkey

Chang-Sik Ha,     Pusan National University, Busan, Korea

Alok Kalra,     CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India

Kummari S.V. Krishna Rao,     Yogivemana University, Kadapa, India

Hitesh Kulhari

CSIR-Indian Institute of Chemical Technology, Hyderabad, India

Central University of Gujarat, Gandhinagar, India

Piyush Kumar,     Indian Institute of Technology Bombay, Mumbai, India

Xue Li,     Université Paris-Sud, Orsay, France

Seema Mehdi,     JSS University, Mysuru, India

Marius Mioc,     University of Medicine and Pharmacy Victor Babes Timisoara, Eftimie Murgu, Romania

Arunachalam Muthuraman,     JSS University, Mysuru, India

I. Nowak,     Adam Mickiewicz University in Poznań, Poznań, Poland

Fatma Duygu Özel Demiralp,     Ankara University, Ankara, Turkey

A. Yekta Ozer,     Hacettepe University, Ankara, Turkey

Sibel A. Ozkan,     Ankara University, Ankara, Turkey

Akash K. Patel,     CSIR-National Botanical Research Institute, Lucknow, India

Vikas K. Patel,     CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India

I. Pereira

University of Coimbra, Coimbra, Portugal

University of Trás-os-Montes and Alto Douro, Vila Real, Portugal

Iulia Pinzaru,     University of Medicine and Pharmacy Victor Babes Timisoara, Eftimie Murgu, Romania

Deep Pooja,     CSIR-Indian Institute of Chemical Technology, Hyderabad, India

Kummara Madhusudana Rao,     Pusan National University, Busan, Korea

Narahari Rishitha,     JSS University, Mysuru, India

Prasant K. Rout,     CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, India

A.C. Santos,     University of Coimbra, Coimbra, Portugal

Khan M. Sarim,     CCS Haryana Agricultural University, Hisar, India

Ceyda T. Sengel-Turk,     Ankara University, Ankara, Turkey

Mine Silindir-Gunay,     Hacettepe University, Ankara, Turkey

A.M. Silva,     University of Trás-os-Montes and Alto Douro, Vila Real, Portugal

Ramakrishna Sistla,     CSIR-Indian Institute of Chemical Technology, Hyderabad, India

Cassian Sitaru

University of Freiburg, Freiburg, Germany

BIOSS Centre for Biological Signalling Studies, Freiburg, Germany

Codruta Soica,     University of Medicine and Pharmacy Victor Babes Timisoara, Eftimie Murgu, Romania

E.B. Souto,     University of Coimbra, Coimbra, Portugal

Cristina Trandafirescu,     University of Medicine and Pharmacy Victor Babes Timisoara, Eftimie Murgu, Romania

Seçil Karahisar Turan,     Hacettepe University, Ankara, Turkey

Bengi Uslu,     Ankara University, Ankara, Turkey

F.J. Veiga,     University of Coimbra, Coimbra, Portugal

Hatice Yildizhan,     Ankara University, Ankara, Turkey

A.T.M. Zafrul Azam,     University of Dhaka, Dhaka, Bangladesh

A. Zielińska

Adam Mickiewicz University in Poznań, Poznań, Poland

University of Coimbra, Coimbra, Portugal

Series Preface: Pharmaceutical Nanotechnology

Alina M. Holban, University of Bucharest, Bucharest, Romania

Due to its immense applicative potential, nanotechnology is considered the leading technology of the 21st century. The science and engineering of nanometer-sized materials is currently employed for the development of numerous scientific, industrial, ecological, and technological fields. Biology, medicine, chemistry, pharmacy, agriculture, food industry, and material science are the main fields which have benefited from the great technological progress developed in nanoscience.

In the pharmaceutical field, nanotechnology has revolutionized traditional drug-design concept and the art of drug delivery. The idea of a highly specific nanoscale drug for the targeted therapy of diseases is now considered a feasible treatment for severe health conditions.

Some scientists believe that the pharmaceutical domain has been reborn by the important contribution of nanotechnology. The field of pharmaceutical nanotechnology has the potential to offer innovative solutions for all diagnosis, therapy, and prophylaxis domains. Application of nanotechnology tools in pharmaceutical research and design is likely to result in moving the industry from a blockbuster drug model to personalized medicine. The current main focus of clinicians is to treat patients individually, not their general diagnosed diseases, which are usually difficult to diagnose or incorrectly diagnosed. There are compelling applications in the pharmaceutical industry where suitable nanotechnology tools can be successfully utilized. By designing and modifying drugs at nanoscale, pharmaceutical nanotechnology could be useful not only for the development of completely new therapeutic solutions, but also to add value to existing products. This possibility opens perspectives of success for pharmaceutical companies in existing markets, but also for new markets.

Scientists have manifested an impressive interest on the field of pharmaceutical nanotechnology research in recent years. However, we face today a true dilemma of data unavailability, due to the multitude of existing information which can be highly inaccurate and contradictory. This is because of the lack of an efficient model for sorting the plethora of nanotechnology tools and information that exists, and strategically correlate those with potential opportunities into different segments of pharmaceutical research and design.

This series is trying to cover the most relevant aspects regarding the great progress of nanotechnology in the pharmaceutical field and to highlight the currently emerging trend of pharmaceutical nanotechnology towards the personalized medicine concept.

The 10 volumes of this series are structured to wisely offer relevant information regarding basic concepts and also to reveal the newest approaches and perspectives in pharmaceutical nanotechnology.

Nanoscale Fabrication, Optimization, Scale-Up and Biological Aspects of Pharmaceutical Nanotechnology, introduces the readers into the amazing field of nanoscale design. Also, this volume facilitate understanding of the biological requirements of nanostructured pharmaceutical formulations for advanced drugs.

In Design and Development of New Nanocarriers, the most recent progress made on the field of nano-delivery is discussed. Modern nanostructured drug carriers employ innovative solutions for the detection and treatment of various diseases in a personalized and efficient manner.

Design of Nanostructures for Theranostics Applications, highlights the impressive impact of nanotechnology in the development of combined diagnosis and therapy concept: theranostics.

Design of Nanostructures for Antimicrobial, Antioxidant and Nutraceutical Applications, offers a dynamic solution for immune modulation, treatment of diseases by natural-based products and infection control, while employing nanostructured solutions to achieve top results.

Nanostructures for the Engineering of Cells, Tissues and Organs: From Design to Applications, is a highly investigated and debated field; tissue engineering, is dissected through this volume. Here is shown how nanotechnology has advanced research and applications in the manipulation and engineering of cells and tissues in vitro.

Organic Materials as Smart Nanocarriers for Drug Delivery, deals with the specific world of organic nanomaterials, revealing their wide applications, types, and advantages in drug delivery.

In the volume entitled: Inorganic Frameworks as Smart Nanomedicines, the main focus is to discuss the variety and properties of inorganic nanostructures for therapy and drug delivery in the context of improved personalized medicine.

Lipid Nanocarriers for Drug Targeting, deals with recently developed lipid nanostructures and the advances made in drug targeting.

Drug Targeting and Stimuli-Sensitive Drug Delivery Systems, dissects smart stimuli-responsive nanosystems employed to specifically detect various biochemical conditions and control the release of drugs.

Fullerens, Graphenes and Nanotubes: A Pharmaceutical Approach, reveals major findings made on widely applied drug-design nanosystems, namely fullerens, graphenes and nanotubes. The impact of these nanostructures in pharmaceutical research is highlighted.

All 10 volumes are nicely illustrated and chapters are organized into a logical manner to be accessible to a wide audience. The series is a valuable resource of new and comprehensive scientific proof on the intriguing and emerging field of pharmaceutical nanotechnology, which could be of a great use for scientists, engineers, pharmaceutical representatives, clinicians, and any non-specialist interested user.

Preface

Alexandru M. Grumezescu, University Politehnica of Bucharest, Bucharest, Romania

The aim of this book is to present the innovative progress performed in the recent years in the field of nanostructures with theranostic applications. Special attention is assigned to the multifunctional nanoparticles for diagnostics and treatment of different diseases. Different types of nanostructures are discussed in detail regarding design, fabrication, functionalization, and optimization in order to obtain desired properties.

This book, entitled Design of nanostructures for theranostics applications, contain 16 chapters, prepared by outstanding researchers from Turkey, Norway, Macedonia, Romania, Germany, India, United States, Poland, Portugal, and Bangladesh.

Chapter 1, Novel diagnostic techniques: genomic, proteomic and systems biology approaches, prepared by Seçil Karahisar Turan et al., gives an up to date overview about cancer theranostics in order to decrease the latencies in treatment by combining diagnosis and therapy. The main objectives of cancer theranostics include identification of novel biomarkers for molecular diagnosis of different cancer types, developing molecular imaging probes, new techniques for early detection of cancer, and utilizing nanotechnology and molecular imaging for both imaging and treatment.

Chapter 2, Nanotheranostics and theranostic nanomedicine for diseases and cancer treatment, prepared by Catalano Enrico, presents the recent progress in the field of nanotheranostics and theranostic nanomedicine. These allows an integrative approach related to diagnostic and therapeutic properties in one single entity to pursue an extremely innovative personalized medicine for diseases and cancer treatment. Nanotheranostics have three main properties: nano-dimensions, therapeutic effect, and diagnostic agent. Several types of nanocarriers were developed so far for nanotheranostics, which include dendrimers, liposomes, micelles, polymer conjugations, metal and inorganic nanoparticles, solid lipid nanoparticles, and carbon nanotubes.

Chapter 3, A novel approach for drug targeting: core–shell type lipid–polymer hybrid nanocarriers, prepared by Ceyda Tuba Sengel-Turk et al., describes the importance and the place of core–shell type lipid–polymer hybrid nanosystems as a novel drug targeting strategy. Some selected applications that have been realized within past 10 years were also investigated from an analytical point of view, such as evaluation of the preparation technologies, in vitro and in vivo characterization parameters of these nanocarriers.

Chapter 4, Multifunctional core–shell polymeric and hybrid nanoparticles as anticancer nanomedicines, prepared by Nikola Geskovski et al., focuses on the major classes of core–shell nanoparticle platforms (i.e., amphiphilic block co-polymer CS (core-shell) nanoparticles, polymer–polypeptide hybrid CS nanoparticles, polymer–lipid hybrid CS nanoparticles), their optimal design for successful solid tumor targeting, efficacy and safety, as well various targeted drug delivery applications. The contributors also review the porous metal-organic framework (MOF) nanoparticles (nano-MOFs) that have been developed for drug delivery, thus offering a way to solve some of the limitations of polymer nanocarriers through their unique structure, high surface area, and large pore sizes, empowering efficient loading of various types of pharmaceuticals and diagnostic agents.

Chapter 5, Silver-, gold-, and iron-based metallic nanoparticles: biomedical applications in cancer as theranostic agents, prepared by Codruta Soica et al., provides a systematic search of the main biomedical applications as theranostic agents in cancer of three types of metallic nanoparticles, based on silver, gold and iron/iron oxide, also offering an insight on future perspectives. The chapter emphasizes the most recent advances in the antitumor use of metallic nanoparticles. The chapter also includes several reviews, focused on the same topic, in order to highlight the novel aspects introduced therein.

Chapter 6, Functional stimuli-responsive polymeric network nanogels as cargo systems for targeted drug delivery and gene delivery in cancer cells, prepared by Kummara Madhusudana Rao et al., gives an up to date overview about recent progress on nanogel drug delivery systems for targeted drug delivery and gene delivery in cancer cells. In this chapter, they briefly analyze the role of drug delivery systems, importance of nanogels in the targeted drug delivery, stability in the extracellular and intracellular environment, cellular uptake behavior, internalization in the cells, degradation behavior in the cells, and the transfection efficiency of nanogels. This chapter also covers the advantages and drawbacks of responsive nanogels and future outlooks for targeted drug delivery and gene delivery in cancer cells.

Chapter 7, Dendrimer-drug conjugates: synthesis strategies, stability and application in anticancer drug delivery, prepared by Deep Pooja et al., focused on the advantages and strategies for the synthesis of dendrimer-drug conjugates (DDCs) and their characterization. It also highlights the stability of DDCs in the biological system and their effect on the efficacy of the conjugated drug molecule, compared to pure drug. In the end, it enlightens DDC-mediated solubility enhancement and alteration in pharmacokinetics of anticancer drugs, and the development of targeted DDCs for the selective delivery of anticancer drugs to tumors.

Chapter 8, Liposomes and micelles as nanocarriers for diagnostic and imaging purposes, prepared by Mine Silindir-Gunay et al., gives an overview about the early diagnosis of a variety of diseases that is crucial for early therapy, therapy monitoring, and therapy staging. The use of relatively new developed imaging modalities and hybrid imaging systems requires the need for better, high contrast, localized radiocontrast/contrast imaging agents. Multifunctional nanocarriers are very promising systems for specific molecular imaging. Nano-sized liposomes and micelles can also be used for both diagnosis and therapy of several diseases as theranostics. The improvement in these specific imaging nanocarriers can help nuclear medicine and radiology physicians to diagnose and image disease sites early and more accurately.

Chapter 9, Small RNA-mediated prevention, diagnosis, and therapies of cancer, prepared by Abdullah Al Hasan et al., presents recent progress in cancer-associated aberrant RNAs, as new methodology for their detection and the impact on expression of oncogenes and tumor suppressor genes. The potential of developing therapeutics using small RNAs to modulate cancer-associated defects and advances in the delivery of small RNAs are also discussed. Finally, clinical perspectives of studying RNA defects in cancer are discussed, together with their relevance to cancer development, prevention, diagnosis, therapies, and treatment resistance.

Chapter 10, Mesoporous silica nanoparticles as drug delivery systems against melanoma, prepared by Zielińska, A. et al., gives a comprehensive account of the physicochemical properties of mesoporous silica nanoparticles and describes the synthesis methods for controlling their properties and surface functionalization. In vitro and in vivo biocompatibility studies are also described. Their huge potential as biocompatible and stimuli-responsive drug delivery systems, aiming for site-specific delivery and intracellular controlled drug release, is discussed. The significance of their application against melanoma is particularly emphasized, highlighting their importance in cancer therapy.

Chapter 11, New approaches in breast cancer–targeting pharmaceuticals, prepared by David Aebisher et al., presents an up to date overview about breast cancer treatments that are used in current therapies. Treatment for ductal carcinoma in situ, a non-invasive breast cancer and treatment for invasive breast cancer were reviewed, along with combinations of radiation therapy, chemotherapy, hormone therapy, and targeted therapy. In addition, research studies in the field of prevention and treatment of breast cancer with dietary nutrition, vitamins, supplements, and herbs were discussed. The progress in detection of breast cancer biomarkers and their response to systemic therapy were discussed, along with identification of new targets for drug treatment, such as chemotherapeutics and monoclonal antibodies.

Chapter 12, Conventional and current imaging techniques in cancer research and clinics, prepared by N. Pinar Barkan et al., gives an overview about the prevalent use of macroscopic imaging systems in preclinical and clinical applications: computed tomography (CT), magnetic resonance imaging (MRI) and ultrasound, and recently emerging molecular imaging systems: positron emission tomography, single-photon-emission CT, and hybrid technologies are described. Novel technologies, such as bioluminescence imaging, near infrared fluorescence, and photoacoustic imaging are also explained.

Chapter 13, Imaging, molecular diagnostics and cancer treatment, prepared by Arunachalam Muthuraman et al., presents recent progress in the understanding of nanoparticle usage in the diagnosis and treatment of cancer disorders. They discuss the interactions and/or competition of nanoparticles with the cellular and molecular components of a biological system, including cancer cells, that allows the early detection of diseases such as cancer. The biomedical imaging system also supports the identification of different cancer cell properties, with increase of specific selectivity and reduction of nonspecific cellular uptake. This is due to its high spatial resolution of nanoparticle with targeted ligands.

Chapter 14, Synthetic microbial ecology and nanotechnology for the production of taxol and its precursors: a step towards sustainable production of cancer therapeutics, prepared by Vikas Kumar Patel et al., presents the recent progress of synthetic microbial ecology and nanotechnology that have been explored to produce the anticancer compounds, paclitaxel and baccatin, through developing synthetic consortia of endophytes from Taxus plant. It elaborates on applying magnetic affinity nanobeads, nanodevices, and nanochips in their fermentation broth for easier recovery and its development as a sustainable microbial nanotechnology for cancer therapeutics.

Chapter 15, Current trastuzumab drug delivery systems for magnetic resonance imaging detection, prepared by Dorota Bartusik et al., reviews the development of the trastuzumab delivery system by synthesis, and evaluation of trastuzumab drug delivery systems using MRI and MR spectroscopy (MRS). The contributors also present a discussion of the pharmaceutical efficiency of trastuzumab drug delivery systems and give an overview about other currently used immunotherapeuticals which have potential to be used in drug delivery systems.

The main rationale of this study is to investigate the utility of ¹H/¹⁹F MRI and ¹H/¹⁹F MRS on tracking and visualization of trastuzumab conjugates on the cellular level. The strategies and methodologies discussed in this chapter present the ability to visualize drug uptake by cancer tissue and to quantify the response of tissue to treatment. This chapter also reviews new drug delivery systems which impact drug resistance and human health.

Chapter 16, Recent advancement in cancer treatment, prepared by Piyush Kumar, discuss recent advancement in cancer immunotherapy, epigenome therapy, surgery (including plastic surgery), robotic radiotherapy, and hormonal and photothermal therapy for cancer treatment. The chapter has also elucidated the advantages and limitations of each of these therapies and presents an update on clinical trials. In addition, the chapter has emphasized the importance of multimodal imaging and three-dimensional (3D) imaging technology in combinational therapy and reconstitutive surgery for effective cancer theranostics.

www.grumezescu.com

Chapter 1

Novel diagnostic techniques

Genomic, proteomic and systems biology approaches

Seçil Karahisar Turan¹, Hatice Yildizhan², Nezahat Pinar Barkan¹, Fatma Duygu Özel Demiralp², Bengi Uslu² and Sibel A. Ozkan²,    ¹Hacettepe University, Ankara, Turkey,    ²Ankara University, Ankara, Turkey

Abstract

Many cancer types still cause mortality because of late and/or wrong diagnosis. Cancer is a heterogeneous disease of which prognosis, prediction, and treatment cannot be easily achieved. This is why standardized cancer treatment may not be effective, even in members of the same family. Therefore, the necessity of applying personalized cancer therapies has emerged. Molecular diagnostics aim to get patient specific information by genomics-based, proteomics-based molecular profiling assays and systems biology approaches.

Cancer theranostics aim to decrease the latencies in treatment by combining diagnosis and therapy. The main objectives of cancer theranostics include identification of novel biomarkers for molecular diagnosis of different cancer types; developing molecular imaging probes and new techniques for early detection of cancer; and utilizing nanotechnology and molecular imaging for both imaging and treatment. With the appropriate applications in personalized oncology, more accurate diagnosis and therapies will be achieved in the right time, to the right cancer patient. To succeed in this approach, the enhancement of theranostic biomarkers is crucial. Advances in molecular biology techniques, such as genome sequencing and omics technologies, provide high-throughput data on the underlying molecular pathways of different cancer types. In accordance with the developments in these tools, more reliable and novel molecular biomarkers can be designated which may be more effective in cancer diagnosis and treatment.

Keywords

Cancer diagnostics; genomics; proteomics; systems biology; cancer theranostics; nanomedicine; nanotechnology; tumor biomarkers; biosensors

Chapter Outline

1.1 Introduction 2

1.2 Molecular Diagnostics Era 4

1.2.1 Molecular Diagnosis of Cancer 6

1.3 Molecular Technologies for Cancer Diagnostics 7

1.3.1 Polymerase Chain Reaction-Based Methods 7

1.3.2 Electrophoretic Methods Used for Mutation Analysis and Cancer Diagnostics 8

1.3.3 Molecular Imaging 9

1.3.4 Microarray Technologies 10

1.3.5 Next Generation Sequencing Technology in Cancer Diagnostics 10

1.3.6 RNA Splicing Events in Cancer 11

1.3.7 Using Epigenetic Alterations in Cancer Diagnosis 12

1.3.8 Effect of Somatic Mutations in Cancer 13

1.4 Cancer Theranostics 14

1.4.1 Genomics-Based Cancer Theranostics 15

1.4.2 Proteomics-Based Cancer Theranostics 15

1.4.3 Current Proteomics Biomarkers for Cancer 17

1.4.4 Systems and Network Biology Approaches 22

1.4.5 Key Functional Pathways in Cancer 26

1.4.6 Cancer Biomarkers 30

1.5 Nanotechnologic Approaches in Cancer Diagnostics 31

1.5.1 Biosensors 32

1.6 Clinical Applications 33

1.7 Future Aspects of Molecular Diagnostic Tools 34

1.8 Conclusion 36

References 36

1.1 Introduction

Cancer is a complex and heterogeneous disease, which shows major characteristic differences between patients and also in tumors of the same patient. A group of diseases, which are classified as cancer, are basically characterized with uncontrolled cell division. Both intrinsic and extrinsic factors can be responsible for development of cancer (Torre et al., 2015).

Cancer remains one of the major causes of morbidity and mortality all over the world (Bray et al., 2012). As stated in the World Cancer Report 2014, number of new cancer cases was 14.1 million, and 8.2 million deaths were caused by cancer around the world in 2012 (Stewart and Wild, 2016).

Cancer affects all people around the world, but there are differences between nations, regions and also genders, especially in the incidence of tumor types. While high income countries provide the best opportunities for detection, diagnosis and treatment of cancer, the highest incidence and prevalence are also seen in these populations. Cancer is the second disease, following cardiovascular diseases, leading to death in high resource countries; and third in low- and middle-income countries, following cardiovascular and parasitic diseases (Bray et al., 2012; Stewart and Wild, 2016; Torre et al., 2015).

The estimated number of new cancer cases by 2030 is 21.7 million and the number of deaths related to cancer is expected to be 13 million. Researchers noted that these estimations will be higher due to the changes in lifestyles, which will increase the risk of getting cancer. Smoking, unhealthy diets, physical inactivity and fewer pregnancies are included in the factors that increase the risk of cancer in economically developing countries. The incidence of different cancer types can be changed due to the economical status of the countries. While the incidence of breast, lung and colorectal cancers are rising in economically transitioning countries; lung, prostate and colorectal cancers among men and breast, lung and colorectal cancers among women are more common in economically developed countries (Fig. 1.1). Furthermore, the most common cancer types diagnosed in males of economically developing countries are liver, lung and stomach and in females lung, cervix uteri and breast cancers (Bray et al., 2012; Jemal et al., 2010; Stewart and Wild, 2016; Torre et al., 2015).

Figure 1.1 Cancer types distribution scheme according to the Human Development Index (HDI) level. (A) Number of new cases, (B) lifetime cumulative risk of incidence, (C) number of deaths, (D) lifetime cumulative risk of death. Reprinted from Bray, F., Jemal, A., Grey, N., Ferlay, J., Forman, D., 2012. Global cancer transitions according to the Human Development Index (2008–2030): a population-based study. Lancet Oncol., 13, 790–801, with permission from Elsevier.

The World Health Organization (WHO) developed a global action plan for the prevention and control of noncommunicable diseases, such as cancer, diabetes, cardiovascular diseases, and chronic respiratory diseases for the period of 2013–20. The main goal of this action plan is reducing the morbidity, mortality, and disability caused by these diseases by national, regional and global scale, multisectoral collaborations and cooperations. They also intended to increase the health standards, quality of life, and productivity at all ages (World Health Organization, 2013).

The advancements in molecular biology and biotechnology bring a new perspective to cancer, especially by introducing novel techniques in diagnostics, prognosis, and treatment strategies. According to the World Cancer Report 2014, studies of the past 5 years paved the way for identification of several cancer pathways from many tumor types by using whole-genome sequencing and omics technologies, such as genomics, proteomics, transcriptomics, and metabolomics. These data are critical for understanding the nature of cancer, and are evaluated to provide early detection opportunities, to develop highly effected therapeutic strategies and eventually to reduce cancer mortality (Stewart and Wild, 2016).

1.2 Molecular Diagnostics Era

The combination of laboratory medicine with molecular genetics technology showed fundamental changes in recent years. Molecular applications of human diseases facilitate detection, diagnosis, classification, prognosis, and monitoring the progress of disease or the responses to applied therapy. The molecular disease term was introduced to the medical society by Pauling and his colleagues, in 1949. They have discovered a single amino acid change at the β-globin chain of hemoglobin, which causes sickle cell anemia. While their findings are accepted as the foundation of molecular diagnostics, the main developments of this field occurred many years later (Patrinos and Ansorge, 2010).

The advancements of recombinant DNA technology, developing DNA probes and Southern blot analysis of certain genomic regions, cDNA cloning and sequencing, applications of restriction fragment length polymorphism (RFLP) for tracking a mutant allele gradually improved the usage of molecular techniques in screening and diagnosis of many diseases. Most of the first attempts are based on finding the disease-causing mutations. In the following years, several mutations have been found, by using methods such as mismatch detection in DNA/DNA or RNA/DNA heteroduplexes. As a result of these efforts, many short synthetic oligonucleotides have been designed, which were used in genomic Southern blot assays as allele-specific probes. In spite of these great developments, the golden era of molecular diagnostics starts with the discovery of the polymerase chain reaction (PCR). Through the discovery of PCR, the required time for identification of a known mutation has decreased to only a single day. In the following years, enzymatic based methods, such as RFLP analysis; electrophoretic techniques, such as denaturing gradient gel electrophoresis (DGGE) and temperature gradient gel electrophoresis (TGGE); and solid phase based techniques, such as DNA oligonucleotide microarrays, are started to use for detecting the disease-causing mutations (Patrinos and Ansorge, 2010; Farkas, 2014).

The achievement of the Human Genome Project (HGP) and identification of the genomic sequences of other organisms, provided new opportunities and challenges to molecular biology research. These developments led to producing huge amounts of data, which can only be analyzed by specialized software. New methodologies have been evolved to obtain rapid, relevant cost, and high-throughput analyses of gene-based variations for detecting the mutations. One of the most powerful techniques for mutational analysis is denaturing high-performance liquid chromatography. Real-time PCR is another technique, which is more rapid, sensitive, and reproducible than PCR. DNA microarray-based genotyping approach can also analyze many polymorphic regions and sequence alterations simultaneously, and facilitates genome-wide screening. Development of proteomics-based techniques provides a significant contribution to molecular diagnostics. Protein-based disease diagnostic tools can be varied, from two-dimensional protein gels to mass spectrometers and high-throughput protein microarrays (Patrinos and Ansorge, 2010; Coleman and Tsongalis, 2007).

The successful conclusion of HGP will lead to launching a global Human Proteome Project (HPP), which aims to map the complete set of human proteins. The general experimental set of HPP is based on mass spectrometry (MS), antibody capture and bioinformatics tools. The results of this project will enhance the knowledge about biological structures of humans at the cellular level and provide opportunity to develop novel diagnostic, prognostic, therapeutic, and preventative applications for many diseases, including cancer. The prime purpose of the project is to determine and characterize at least one protein product and many posttranslational modifications, splice variant isoforms, and single amino acid polymorphisms from the 20,300 human protein coding genes. The collaboration of approximately 50 international research groups has been generating a gene-centric parts list of the human body, which is termed as Chromosome-centric HPP. These researchers want to integrate proteomic data through a genomic scheme, which will enhance our knowledge about biological systems and make protein level information easily accessible. Concurrently, a complementary study to enlighten the protein-based molecular structures of healthy and diseased systems is being conducted, which is termed as Biology/ Disease HPP (B/D HPP). The Human Cancer Proteome Project project is a part of B/D HPP, which aims to analyze cancer-related molecular networks. They focus on identifying specific, sensitive protein biomarkers or cancer-associated proteins by using MS, microarray techniques, or antibody capture, to share these target proteins or isoforms in a convenient data portal for validation and clinical application (Cantor et al., 2015; Eckhard et al., 2016; Legrain et al., 2011; Omenn, 2014).

Molecular diagnostics enable the screening of large populations by using genetic tests. It can be also used as a complement to clinical trials. The molecular techniques that are used for diagnosis can be classified as, PCR-based methods, non-PCR methods, gene chip and microfluidic microarrays, nanodiagnostics, toxicogenomics, single nucleotide polymorphism (SNP) genotyping, DNA methylation studies, gene expression-based tests, DNA sequencing, cytogenetics, proteomic-based methods, microRNA-based methods, and molecular imaging techniques. The use of molecular techniques for diagnosis are thought to be a milestone for providing better treatment strategies for several diseases. Understanding the molecular mechanisms of diseases will pave the way for personalized medicine applications (Jain, 2015).

1.2.1 Molecular Diagnosis of Cancer

More than 200 diverse diseases are classified as cancer. The complexity of cancer comes from the histologic structure of tumors that consists of normal epithelium cells, premalignant cells, stroma and inflammatory exudates, and also from many molecular changes and mutations. Cancer can be described as the uncontrolled and unlimited division of cells that cause invasion to adjacent tissues and metastasis to distant organs. Modifications of the DNA sequences of certain genes result in gene or protein expression variations. The accumulation of these DNA alterations causes progressive dysregulation of cancer cells and paves the way to uncontrolled proliferation of cancer (Herold and Rasooly, 2012).

The traditional way of in vitro diagnostics of cancer mainly depends on microscopic investigations of tumor tissues or cells. Researchers have been focused on the metabolism, enzymes and other characteristics of tumor cells. A number of scientists realized in the 1920s that, some kind of genetic mutations transform normal cells to cancerous ones. Unfortunately, the technology has not been adequate to test these claims on these days. The advancements on molecular biology, cell biology, molecular genetics, and cytogenetics have led to develop novel methodologies that can be used in cancer diagnosis (Wagener and Neumann, 2012).

Up until a short time ago, molecular diagnosis of cancer has mainly relied on investigating the most frequent mutations and using low-throughput molecular and cytogenetic methods, which can only analyze a limited number of mutations or target regions simultaneously. Nevertheless, a lot of mutations and genes related with many cancer types have been identified over the years. In light of this information, instead of studying with one gene or mutation, using next generation sequencing (NGS) technology to test parallel multigenes is preferred (Ankala and Hegde, 2014).

The success of personalized therapies for cancer depends mostly on the accuracy of the detected mutations before treating them (Sawyers and van‘t Veer, 2014). Scientists and clinicians are looking forward to find rapid, sensitive, noninvasive, and more accurate diagnostic tests to detect and treat many cancer types. To win the battle against cancer, researchers should focus on preclinical disease detection, which may enable starting treatment before cancer metastasizes and becomes incurable (van der Merwe et al., 2006). The scientific developments of genomics, proteomics, and other omics technologies provide reliable tools to improve the early detection tools and treatment strategies of several cancers(Sawyers and van‘t Veer, 2014). The advancements of biosensors, the analytical devices that use biological ligands, such as antibodies, peptides or aptamers, are considered to provide several potential advantages on cancer detection in the near future (Herold and Rasooly, 2012). Hybrid strategies, which are combinations of imaging technologies with other modalities such as biomarkers, are thought to be better tools for early and correct diagnosis of cancers (van der Merwe et al., 2006).

1.3 Molecular Technologies for Cancer Diagnostics

Technological developments lead to advancements in diagnostics methodologies of cancer, too. Current molecular diagnostics technologies used for cancer diagnosis can be classified as PCR-based methods, arrays and microarrays, enzyme-based methods, gene chip technologies, SNP genotyping, microRNA-based technologies, DNA methylation, gene expression-based technologies, DNA sequencing, cytogenetics, proteomic-based strategies, immunohistochemical analysis molecular imaging, and nanotechnologic applications (Jain, 2015; Tan and Lynch, 2012). Each method has its pros and cons, and researchers are still working to develop novel strategies for the early diagnosis of cancer. As a consequence, selecting the appropriate method before clinical application has considerable importance for a successful diagnosis or treatment.

DNA/RNA sequencing becomes a routine molecular diagnostics tool in several research and clinical laboratories for screening genetic diseases. DNA microarrays are timesaving, sensitive and cost-effective methods for sequencing and analyzing genes. For earlier detection and prognosis of many cancers, comparative gene expression profile analysis of healthy and diseased cells can be performed by using this technique. Nucleic acids are mostly used as target molecules in biochip technology, however protein chips also have great importance for distinguishing the healthy cells from malignant and metastatic cells or for staging the cancer (Jain, 2015; Tan and Lynch, 2012).

The investigation of nucleic acids, proteins, metabolites and other functional parameters in a single-cell level are the subjects of cytogenetics. Molecular cytogenetics has a prominent position in molecular diagnostics. Advancements in cytogenetics lead to novel methodologies, such as fluorescent in situ hybridization (FISH) and array-based techniques that allow more detailed evaluations of the molecular basis of structural chromosomal anomalies. SNPs are frequently used as markers for identifying the genetic risk profiles of several cancer types. Haplotyping is another method for SNP genotyping. A list of common SNPs in human populations is prepared by the International HapMap Project. Using nanotechnologic materials, devices, and systems in life sciences opens up new perspectives in molecular diagnostics. Developments in nanodiagnostics will cross the borders of molecular diagnostics, by enabling the direct examination, management, and analysis of a unique biological molecule in an individual cell (Jain, 2015).

1.3.1 Polymerase Chain Reaction-Based Methods

Most of the mutation detection assays depend on PCR technique. In general, PCR is not the main method for direct mutation detection, but amplicons that are generated by PCR are analyzed with other techniques to detect mutations. These techniques include sequencing, single-stranded conformational polymorphism (SSCP), DGGE. Furthermore, methods comprising a modified PCR, such as real-time PCR, quantitative fluorescent PCR(QF-PCR), the amplification refractory mutation system (ARMS), or multiplex ligation-dependent probe amplification (MLPA) can be used as primary mutation detection assays. However, the majority of these methods can only find out the mutations which have been previously detected and characterized by other methods. The only PCR-based method that doesn’t need any additional technique to detect mutations is real-time PCR analysis. Real-time PCR analysis is mainly performed for SNP genotype analysis and determines the copy numbers of specific target sequences in molecular diagnostics laboratories. Real-time PCR can also be used for detecting DNA methylation, which is an important mechanism for cancer diagnosis. Its rapidity and having no post-PCR steps are the benefits of real-time PCR method. ARMS is mainly used for detecting point mutations and small insertions/deletions; ARMS assays are rapid and inexpensive, however they cannot be used for screening unknown mutations (Coleman and Tsongalis, 2007).

Two types of PCR-based technologies, which are tumor clonality assay and cold PCR, are used especially in molecular oncology (Tan and Lynch, 2012). PCR is routinely used for identifying mutations of oncogenes and anti-oncogenes. For instance, PCR is used for diagnosing chronic myelogenous leukemia by analyzing bcr/abl fusion, and also for detecting ras point mutations to identicate the tumor progression markers. Consequently, the developments of PCR-based technologies have greatly expanded the current knowledge about cancer development and tumorigenesis (Wagener and Neumann, 2012).

1.3.2 Electrophoretic Methods Used for Mutation Analysis and Cancer Diagnostics

PCR applications are frequently used for the diagnosis of inherited, infectious and, hematological diseases. There are several PCR-based mutation-detection techniques, which are currently used for analysis of defined and undefined mutations, and sequence variations. Most of the mutation analysis including a PCR step uses PCR to amplify the specific DNA regions, which are potential or known mutation carriers. However, some other hybridization or electrophoretic separation techniques are used for distinguishing the normal or mutated DNA sequences, obtained from PCR. Electrophoresis technique is based on the migration of charged molecules under an electric field. The medium, in which these charged molecules move, can be either in liquid or gel phase. This efficacious separation method allows for the sorting of macromolecules, according to their emigrational features. Two commonly used gel matrices are agarose and polyacrylamide (Coleman and Tsongalis, 2007).

Capillary electrophoresis (CE) is another electrophoretic application which is used in molecular diagnostics laboratories. Electrophoresis is performed in thin, fused silica capillary columns. Separated products are detected with various types of detectors. CE provides higher resolutions in comparison to slab gels (Coleman and Tsongalis, 2007). Both small- and macro-molecule biomarkers in complex samples can be analyzed by using CE. CE can be used to identify DNA/RNA point mutations, protein misexpressions, and metabolite abnormalities. There are different types of CE, such as capillary gel electrophoresis (CGE), capillary zone electrophoresis (CZE), and non-gel sieving capillary electrophoresis. Many techniques can integrate with CE systems for biomarker research and monitoring the mechanism of tumorigenesis, such as MS, laser-induced fluorescence (LIF), RFLP, PCR, immunoassay, or ligase detection reaction (LDR). Microchip capillary electrophoresis (MCE) is considered as a very promising tool for biomarker screening in clinical applications. This technique includes sample pre-treatment, separation, and detection systems on a chip. CE and MCE techniques have become favored methods for multiplex biomarker screening studies. Chip-based electrophoretic systems are generally used for investigating low-abundance gene mutations with high sensitivity (Yang and Sweedler, 2014).

1.3.3 Molecular Imaging

Molecular imaging enables the visualization, characterization and quantification of the biological processes of intact living organisms at the cellular and subcellular levels (Luna et al., 2014). Molecular imaging is frequently used to clarify basic biology, diagnose and stage the disease, and assess the in vitro properties of administered drugs (Welch and Eckelman, 2012). One of the most advantageous sides of molecular imaging techniques is the investigation of the biological processes in their own physiological conditions (Chen and Wong, 2014).

The neoplastic process can be monitored noninvasively by using molecular optical imaging (OI) techniques. This approach combines OI with targeted, optically active contrast agents. These targeted, optically active contrast agents enable OI of many cancer biomarkers (Hellebust and Richards-Kortum, 2012).

Noninvasive molecular imaging systems include molecular magnetic resonance imaging (mMRI), magnetic resonance spectroscopic imaging (MRSI), diffusion-weighted MRI (DW-MRI), dynamic contrast-enhanced MRI (DCE-MRI), OI, photoacoustic imaging (PAI), positron emission tomography (PET), single-photon emission computed tomography (SPECT), and ultrasound (US) (Chen and Wong, 2014; Luna et al., 2014).

MRSI is applied to determine tumors according to their metabolic signatures. The DW-MRI technique is based on the water movement in biological tissues. Solid tissues, such as tumors, have higher diffusion-weighted imaging (DWI) signal intensity and lower apparent diffusion coefficient, therefore this technique enables the finding, characterization and staging of tumors, monitoring the response to therapy and recurrence. DCE-MRI acquired images in synch with a contrast agent, passing through the tissues. This method allows scientists to get information about blood flow and vascularization, and is suitable to monitor therapy responses (Luna et al., 2014).

Matrix-assisted laser desorption/ionization-mass spectrometry (MALDI-MS)-based imaging dates back to 1997 (Caprioli et al., 1997). This system defines the localization of peptides and proteins by analyzing thin tissue sections with MS, and the integrated imaging system can monitor the signals from proteins which molecular weights are 2000–200,000 Da. This currently developing technology provides large amounts of data about the protein distributions in different tissues. Expression differences between healthy and cancerous tissues are ongoing investigations for determining novel biomarkers. This imaging technique may become an important tool to represent the surgical margins in real time during the surgical operations (van der Merwe et al., 2006).

1.3.4 Microarray Technologies

DNA microarray technology, in other words a gene chip or DNA chip, allows for the detection of thousands of genes (RNA) or alterations of sequences (DNA) such as SNPs, simultaneously. Small DNA sequences or probes attached to a solid surface, function as molecular targets to cDNA or cRNA for hybridization. This technology is used for both research and clinical applications (Tan and Lynch, 2012).

Major technology platforms which enable gene expression analyses include: Affymetrix GeneChip Technology, spotted arrays, digital micromirror arrays, inkjet arrays, bead arrays and electronic microarrays (Knudsen, 2006).

There are two microarray-based assays which were approved by the US Food and Drug Administration (US FDA) for clinical applications. MammaPrint (Agendia BV, The Netherlands) is used for breast cancer patients to design a personalized treatment strategy. This system is offered as a prognostic test for women under age 61, who have lymph node-negative breast cancer. The genes that can be detected with this system consist of regulators of cell proliferation and invasion, metastasis, stromal integrity, and angiogenesis. The second assay is AmpliChip CYP450 Test (Roche Diagnostics, Pleasanton, CA). CYP2D6 and CYP2C19 genotypes of cytochrome P450 gene are analyzed by this assay. It is a useful test for deciding the most appropriate medicine that has the least side effects (Tan and Lynch, 2012).

1.3.5 Next Generation Sequencing Technology in Cancer Diagnostics

Next generation sequencing technology relies on parallel sequencing and is a timesaving process, compared to Sanger sequencing. Developments of NGS ensure sequencing several genomes from a patient or tumor. These technological advancements promote identifying novel tumor generating mutations, as well as promising diagnostic, therapeutic and prognostic systems (Chen and Wong, 2014).

One of the goals of International Cancer Genome Consortium (ICGC) and The Cancer Genome Atlas (TCGA) project is to list genomic profiles of many cancers. This genomic information collection will help clinicians in determining the heterogeneous texture of tumors and monitor the cancer progression of the patients whom have their complete constitutional and cancer genome sequences, in the near future (Chen and Wong, 2014).

A universal NGS-based oncology test system is developing through participation of pharma companies and Illumina. This system will enable panel-based analysis for selecting cancer therapies. The only NGS-based system that is US FDA-cleared up to now is MiSeqDx. The advancement of this technology will lead to obtaining information about the molecular composition of tumors and match appropriate medicines to the right disease-causing factors (Jain, 2015).

The abnormal nature of tumor cells causes some problems during sequencing. The heterogeneity of tumor genomes and the high degree of chromosomal abnormalities in cancer leads to additional problems while using these techniques. Much effort has been devoted to overcoming these kinds of experimental challenges caused by the nature of cancer cells. For monitoring the disease by using minimally invasive methods, such as tumor DNA detection from the peripheral blood of cancer patients with high sensitivity, novel clinical applications are also developing (Chen and Wong, 2014).

1.3.6 RNA Splicing Events in Cancer

Alternative splicing mechanisms lead to protein diversification. Proteins are dynamic molecules and the biological functions of alternative spliced forms of proteins can differ greatly, even variants can have antagonistic effects. To organize the cellular events in multicellular organisms, controlling these splicing mechanisms is a very important mission. Splicing regulatory mechanisms have many targets for cancer-related deficiencies. Cancer development can be initiated by misregulation of one or a few genes, or cancer-specific splicing alterations in the genes, which are functional in regulation of other genes that can lead to tumorigenesis (Srebrow and Kornblihtt, 2006; Fackenthal and Godley, 2008).

Whole-genome analysis revealed that up to 70% of human genes possibly have alternative splice forms. These alternative splicing mechanisms and posttranslational modifications yield to the complex structure of proteome. While normal cells rarely have aberrant transcripts due to the splicing mechanisms, this is thought to be an intrinsic feature of cancer cells (a et al., 2005).

Inaccurate conditions in mRNA splicing lead to the development of several diseases. Splicing errors can occur due to the somatic or hereditary mutations. Alternative splicing of transcription factors, other cellular factors which have effects on cell signaling, transmembrane proteins, and secreted extracellular proteins are in charge of cancer development. As an example, point mutations in genomic splice sites are seen frequently. High-throughput DNA sequencing and high-density microarrays analyze gene expression and alternative splicing patterns related with tumors. These studies provide information about tumor subtypes that can be used as diagnostic tools and eventually can be important for defining targeted therapies. In a previous study, 29 different p53 splice site mutations are identified in more than 12 different cancer types (Venables, 2004; Fackenthal and Godley, 2008; Kalnia et al., 2005).

Inactivation of the administered drug, high toxicity caused by improper metabolism, or differences in apoptotic thresholds which are required to stimulate cell death are some of the several aspects caused by alternative splicing mechanisms in cancer treatment. Previous studies have showed a correlation between expression differences of alternative apoptotic RNA splice variants in tumors and drug response. Alternative approaches were developed to increase the efficacy of chemotherapeutics by using this mechanism and targeted specific antiapoptotic splice variants. The variations of RNA splicing between tumor biopsies can be screened by using gene expression profiling technologies to develop better treatment strategies (Jain, 2015).

1.3.7 Using Epigenetic Alterations in Cancer Diagnosis

The word epigenetics refers to the variation in gene expression profiles without any modifications in genetic sequences. Epigenetic mechanisms have important functions in natural processes, such as embryogenesis and development, and also have effects on the progress of diseases, like cancer. Recent data obtained from high-throughput analyses present the effects of epigenetic modifications on human carcinogenesis, such as histone modifications, DNA methylation, expression of noncoding RNAs (Taby and Issa, 2010).

Epigenetic mechanisms have an effect on initiation, growth, and progression of cancers. Epigenetic alterations, that are commonly seen in cancer cells include global hypomethylations, histone deacetylations, up-regulation of certain molecules, down-regulation of miRNAs, promoter-specific hymermethylation (Taby and Issa, 2010), nucleosome remodeling and RNA-mediated targeting (Dawson and Kouzarides, 2012). The stable structure of modifications of DNA methylation and miRNA transcription profiles in tissues and body fluids, makes these epigenetic alterations suitable tools for detecting diseases. One of the most stable epigenetic modifications in mammalian tissues is DNA methylation, which can remain stable even in formalin-fixed and paraffin-embedded tissue samples. Observing the DNA methylation alterations are more advantageous than other techniques used for analyzing expression levels of certain genes, such as quantitative RT-PCR, Western Blot and immunohistochemistry, by representing the transcription availability of a target gene and sensitive detection capabilities. Discovering the DNA methylation patterns of critical cells such as cancer stem cells, enable physicians to screen transformation of precancerous lesions to malignant tumors, metastasis, and recurrence of cancer. Investigation of epigenetics and cancer relation is a relatively new field, but some important epigenetic cancer biomarkers, such as methylated H19/Igf2, hMLH1, MGMT, p16, Septin9, have been developed for early diagnosis, prognosis, and observing therapy response of cancers (Deng et al., 2010).

The tumor specific properties of expression level patterns of miRNAs, make them usable tools for early and accurate diagnosis of cancer. The signaling effects of miRNAs on certain genes and gene products regulate the expression levels of miRNAs. While the upregulated miRNAs are thought to have oncogenic potentials, the down-regulated ones in malignancies are potential tumor suppressors. For instance, miR-155, miR-21 and miR-17-92 are examples of miRNAs that have potential oncogenic effects. The overexpression of miR-21 has been reported in several malignancies. The miRNAs with down-regulated expression profiles and tumor suppressor effects in many cancers include the let-7 family and miR-20 (Sethi et al., 2013).

Circulating microRNAs (miRNAs) are considered other promising epigenetic biomarkers, with their high stability in tissues and body fluids. MicroRNAs are small single-strand noncoding regulatory RNAs. The estimated number of miRNA genes in the human genome is up to 1000, which corresponds to about 2%–5% of human genes. miRNAs are functional in the regulation of target genes at transcription or translation level and they are efficient in many biological processes, such as proliferation, differentiation, and apoptosis. Several miRNA genes are founded in the genomic regions which are constantly amplified, deleted, or rearranged in correlation with many cancer types. This state confirms the role for miRNAs in cancer pathogenesis, and monitoring miRNA alteration patterns in cancer development and progression is an emerging field. The potential of miRNAs in early detection, prognosis, and therapy responses of cancers makes them promising cancer biomarkers (Deng et al., 2010).

1.3.8 Effect of Somatic Mutations in Cancer

The commonly seen somatic mutations in cancer cells are single base-pair substitutions, which often result in missense mutations. These type of mutations yield a protein product with a modification in only one amino acid. The frequency of point mutations is similar in normal and tumor cells. However, the rate of large chromosomal abnormalities is much higher in tumor cells than healthy ones (Chen and Wong, 2014).

Whereas the mutations which have minor impacts on affected proteins’ functions or are not important for tumor progression are called passengers; driver "mutations bring growth advantages to the cells and are implicated in oncogenesis. Driver genes are also known as cancer genes. The reason of the presence of passenger mutations in cancer genomes is the somatic mutations which occurred during cell division without functional consequences. The main purpose of cancer genome analysis is to identify the genes that carried driver mutations (Stratton et al., 2009). Oncogenes and tumor suppressor genes are classes of driver genes. Mathematical models consider that cancer development depends on a minimum of 5–8 driver mutations. Nevertheless, the required number of passenger mutations are much more than drivers. For example, the number of protein-altering somatic mutations in common solid tumors are approximately 33–66, but only 3–6 mutated genes in a sample are assumed to be drivers. The excessive number of passengers comparing to drivers makes application of functional tests to detect mutations by NGS difficult. Therefore, advanced bioinformatic tools to predict driver genes and mutations are required. These approaches used the frequency of mutations or prediction of the functional impact of mutations. Thereafter, the most likely candidates selected by bioinformatic analysis will be prioritized for functional testing (Pon and Marra, 2015).

1.4 Cancer Theranostics

From an overall perspective, theranostics is a combination of diagnostics and therapy. In the view of this aspect, cancer theranostics aims to identify new biomarkers to improve molecular diagnostics, develop novel imaging probes and methods for early detection of cancer, and use molecular imaging techniques and nanotechnology for cancer imaging and therapy. The developments of these methods leads to advancements in personalized medicine, which has the potential for targeted therapies and optimized treatment conditions (Chen and Wong, 2014).

Cancer is a heterogeneous disease at both the histological, cellular and molecular levels. Heterogeneity in cancer is not limited to variances between different patients, but also can occur in a single patient. Almost two thirds of mutations detected by single biopsies cannot be found from all over the sampled zones of the same tumor, taken from a single patient (Jain, 2015). This heterogeneity causes important difficulties in diagnosis and treatment of many cancer types. The progression of omics technologies (genomics, epigenomics, transcriptomics, proteomics, metabolomics, etc.), high-throughput assays, and computational methods provide opportunities to reveal the underlying cellular and molecular aspects of cancer. Researchers and clinicians are focused to develop simple, direct and noninvasive diagnostics tests to allow early detection of cancer and apply effective therapies at the right time (Chen and Wong, 2014).

Briefly, molecular alterations that have been examined for diagnosis of different cancer types can be at DNA level, such as gene replication, point mutations and rearrangements; at RNA level, such as transcriptional changes and posttranscriptional modifications; and at protein level, such as translational changes and posttranslational effects (Sethi et al., 2013).

1.4.1 Genomics-Based Cancer Theranostics

Cancer cells divide indefinitely by their nature and can disperse to various parts of the body during metastasis. Clarification of the genomic features of cancer cells and processes will make significant contributions both in diagnostics and drug development. Cancer genomics research dates back many years, but getting cancer-related data at base-pair resolution levels is a relatively new utility. The improvement of NGS technologies turns whole-genome analysis into routine diagnostic tests. While these technologies increase the amount of obtained data from different cancer types and tumors of individual cases, they also decrease the cost per sample dramatically. Meanwhile, the advancement of computational biology overcomes the analyses of these overproduced sequencing data. Accordingly, the genomic basis of common human cancers are getting clearer and detailed statistics about the mutation types, patterns, and phenotypic characteristics exist (Chen and Wong, 2014).

The Cancer Genome Anatomy Project (CGAP) was established by National Cancer Institute (NCI) of the United States for integrating the information technologies and biotechnological tools to understand the molecular features of a cancer cell. The purposes of CGAP were discovering new human genes for enlightening the cancer process, developing methods for detecting cancer at earlier phases, improving strategies for cancer prevention, and promoting classification and diagnosis of cancer (Jain, 2014).

The Human Tumor Gene Index has been prepared with the cooperation of NCI (United States), several academic institutions and companies. As a result of this research, more than 50,000 genes which are functional in one or more cancer types, have been identified.

There are several genomic-based applications, which are used to follow-up certain cancer types, determine mutations or track the lineage of cancer cells. As an example, single-cell FISH