A Beginner's Guide to Targeted Cancer Treatments E-Book

Elaine Vickers

• Herausgeber: John Wiley & Sons
• Kategorie: Fachliteratur
• Sprache: Englisch

Seitenzahl: 885

Veröffentlichungsjahr: 2018

Beschreibung

Highly Commended in the category of Oncology at the British Medical Association Awards 2019 

The accessible guide to the principles behind new, more targeted drug treatments for cancer

Written for anyone who encounters cancer patients, cancer data or cancer terminology, but have no more than a passing knowledge of cell biology. A Beginner's Guide to Targeted Cancer Treatments provides an understanding of how cancer works and the many new treatments available.

Using over 100 original illustrations, this accessible handbook covers the biology and mechanisms behind a huge range of targeted drug treatments, including many new immunotherapies. Dr Vickers translates a complex and often overwhelming topic into something digestible and easily understood. She also explains what cancer is, how it behaves and how our understanding of cancer has changed in recent years.

Each chapter takes the reader through how new cancer drugs work and their benefits and limitations. With the help of this book, readers will be able to better understand more complex, in-depth articles in journals and books and develop their knowledge. This vital resource:

• Offers the latest insights into cancer biology
• Provides a broad understanding of how targeted cancer treatments work
• Describes many of the new immunotherapy approaches to cancer treatment, such as checkpoint inhibitors and CAR-modified T cells
• Helps readers feel confident discussing treatment options with colleagues and patients
• Provides an overview of which treatments are relevant to each of the most common solid tumours and haematological cancers, and the rationale behind them
• Demystifies the jargon – terms such as the EMT, cancer stem cells, monoclonal antibodies, kinase inhibitors, angiogenesis inhibitors etc.
• Explains the resistance mechanisms to many new treatments, including issues such as the way cancer cells diversify and evolve and the complex environment in which they live

Leseprobe

Table of Contents

Cover

About the Author

CHAPTER 1: An Introduction to Cancer Cell Biology and Genetics

1.1 INTRODUCTION

1.2 DNA DAMAGE IS THE CAUSE OF EVERY CANCER

1.3 THE DEFINING FEATURES (HALLMARKS) OF CANCER CELLS

1.4 GENETIC VARIATION AMONG CANCER CELLS IN A SINGLE TUMOR

1.5 THE CANCER MICROENVIRONMENT

1.6 CANCER SPREAD/METASTASIS

1.7 CANCER STEM CELLS

1.8 OBSTACLES THAT PREVENT US FROM CURING CANCER

1.9 FINAL THOUGHTS

REFERENCES

CHAPTER 2: Introducing Targeted Cancer Treatments

2.1 INTRODUCTION

2.2 MONOCLONAL ANTIBODIES

2.3 KINASE INHIBITORS

2.4 FINAL THOUGHTS

REFERENCES

CHAPTER 3: Treatments That Block Proteins Involved in Cell Communication

3.1 INTRODUCTION

3.2 INTRODUCING GROWTH FACTOR RECEPTORS

3.3 DRUGS THAT TARGET EGFR

3.4 DRUGS THAT TARGET HER2

3.5 DRUGS THAT BLOCK OTHER GROWTH FACTOR RECEPTORS

3.6 INTRODUCTION TO SIGNALING PATHWAYS AS A TARGET FOR CANCER THERAPY

3.7 TARGETING THE MAPK SIGNALING PATHWAY

3.8 TARGETING THE PI3K/AKT/MTOR SIGNALING PATHWAY

3.9 TARGETING THE JAK‐STAT PATHWAY

3.10 FINAL THOUGHTS

REFERENCES

CHAPTER 4: Drugs That Target

4.1 ANGIOGENESIS INHIBITORS: INTRODUCTION

4.2 DRUGS THAT BLOCK FUSION PROTEINS: BCR‐ABL, ALK, RET, AND ROS1

4.3 PARP INHIBITORS

4.4 HEDGEHOG PATHWAY INHIBITORS

4.5 CYCLIN‐DEPENDENT KINASE (CDK) INHIBITORS

4.6 FINAL THOUGHTS

REFERENCES

CHAPTER 5: Immunotherapies for Cancer

5.1 INTRODUCTION

5.2 A BIT ABOUT CANCER AND THE IMMUNE SYSTEM

5.3 CHECKPOINT INHIBITORS

5.4 ADOPTIVE CELL TRANSFER

5.5 MODIFIED BI‐SPECIFIC ANTIBODIES

5.6 THERAPEUTIC CANCER VACCINES

5.7 THE FUTURE OF IMMUNOTHERAPY

REFERENCES

CHAPTER 6: Targeted Treatments for Common Solid Tumors

6.1 INTRODUCTION

6.2 TARGETED TREATMENTS FOR BREAST CANCER

6.3 TARGETED TREATMENTS FOR PROSTATE CANCER

6.4 TARGETED TREATMENTS FOR LUNG CANCER

6.5 TARGETED TREATMENTS FOR BOWEL CANCER

6.6 TARGETED TREATMENTS FOR MALIGNANT MELANOMA SKIN CANCER

6.7 TARGETED TREATMENTS FOR KIDNEY CANCER

6.8 TARGETED TREATMENTS FOR HEAD AND NECK CANCER

6.9 TARGETED TREATMENTS FOR BRAIN TUMORS

6.10 TARGETED TREATMENTS FOR BLADDER CANCER

6.11 TARGETED TREATMENTS FOR PANCREATIC CANCER

6.12 FINAL THOUGHTS

REFERENCES

CHAPTER 7: Targeted Treatments for Hematological Cancers

7.1 INTRODUCTION

7.2 A BIT ABOUT HEMATOLOGICAL CANCERS

7.3 ANTIBODY‐BASED TREATMENTS THAT TARGET CD ANTIGENS

7.4 DRUGS THAT BLOCK B CELL RECEPTOR SIGNALING

7.5 BCR‐ABL INHIBITORS

7.6 DRUGS THAT BLOCK THE PROTEASOME

7.7 THALIDOMIDE AND ITS DERIVATIVES

7.8 JAK2 INHIBITORS

7.9 BCL‐2 INHIBITORS

7.10 FLT3 AND KIT INHIBITORS

7.11 IDH2 INHIBITORS

7.12 CAR‐MODIFIED T CELL THERAPY

7.13 FINAL THOUGHTS

REFERENCES

Appendix

Glossary of Terms

Index

End User License Agreement

List of Tables

Chapter 01

Table 1.1 A selection of some of the most commonly mutated oncogenes, tumor suppressor genes, and DNA repair genes in human cancers.

Chapter 02

Table 2.1 Common targets of monoclonal antibody treatments.

Table 2.2 Comparison of different types of kinase inhibitors.

Table 2.3 Targets and uses of kinase inhibitors as cancer treatments.

Chapter 03

Table 3.1 Some of the growth factor receptors implicated in cancer.

Table 3.2 EGFR‐ and HER2‐targeted treatments.

Table 3.3 Comparison of first‐, second‐, and third‐generation EGFR kinase inhibitors.

Table 3.4 Kinase inhibitors that block PDGFRα and KIT.

Table 3.5 Summary of licensed drugs that block the MAPK pathway.

Table 3.6 Summary of B‐Raf inhibitors.

Table 3.7 B‐Raf mutations are found in a range of cancer types.

Table 3.8 Summary of the specificity of various PI3K inhibitors.

Table 3.9 Summary of some mTOR, PI3K, and AKT inhibitors.

Table 3.10 Drugs that block the JAK‐STAT pathway.

Chapter 04

Table 4.1 Angiogenesis inhibitors licensed for use against cancer in the United States and Europe.

Table 4.2 Summary of licensed kinase inhibitors that block VEGF receptors.

Table 4.3 Some of the kinase fusion proteins found in human cancers.

Table 4.4 Comparison of first‐, second‐, and third‐generation ALK inhibitors.

Table 4.5 Characteristics of

BRCA

‐mutated cancers in mutation carriers.

Table 4.6 Summary of the state of development of various PARP inhibitors as of December 2017 (listed in alphabetical order).

Table 4.7 Summary of CDK4/6 inhibitors in phase 3 trials.

Chapter 05

Table 5.1 Mechanisms of different cancer immunotherapies.

Table 5.2 PD‐1 and PD‐L1 targeted antibodies licensed in the United States and Europe as of December 2017.

Table 5.3 Comparison between T cell receptors and B cell receptors.

Chapter 06

Table 6.1 Results from the BOLERO‐2 study of exemestane plus everolimus or placebo in 724 women with hormone treatment‐resistant metastatic breast cancer.

Table 6.2 Results from phase 3 trials investigating a combination of an aromatase inhibitors plus a CDK4/6 inhibitor for the treatment of post‐menopausal women with hormone receptor‐positive (HR‐positive) breast cancer.

Table 6.3 Summary of licensed HER2‐targeted treatments for breast cancer.

Table 6.4 Summary of randomized phase 3 trials investigating PARP inhibitors as treatments for

BRCA

‐mutated breast cancer.

Table 6.5 Summary of randomized phase 3 trials investigating checkpoint inhibitors as treatments for triple‐negative breast cancer.

Table 6.6 Common driver mutations in non‐small cell lung cancers.

Table 6.7 Summary of licensed targeted treatments for lung cancer in the United States and the European Union (EU).

Table 6.8 Results from ALEX trial which involved 303 people with

ALK

‐mutated NSCLC who hadn’t received any prior treatment with an ALK inhibitor.

Table 6.9 Results from the Checkmate 057 trial which involved 582 people with non‐squamous NSCLC who had received prior platinum‐based chemotherapy.

Table 6.10 Summary of licensed targeted treatments for bowel cancer.

Table 6.11 Four‐way classification of bowel cancer.

Table 6.12 People with left‐sided bowel cancers benefit more from EGFR‐targeted antibodies than people with right‐sided bowel cancers; analysis of the CRYSTAL and PRIME trials.

Table 6.13 Licensed targeted treatments for malignant melanoma.

Table 6.14 Results from the CheckMate 067 clinical trial investigating a combination of ipilimumab plus nivolumab in 945 people with previously untreated, metastatic melanoma.

Table 6.15 Results from the OPTiM trial of T‐VEC in people with metastatic melanoma.

Table 6.16 Licensed targeted treatments for renal cell carcinoma (RCC).

Table 6.17 Examples of results from clinical trials that aimed to determine the best second‐line treatment for people with metastatic renal cell carcinoma (RCC).

Table 6.18 Summary of phase 3 trials of checkpoint inhibitors for people with renal cell carcinoma (RCC) as of December 2017.

Table 6.19 Summary of phase 3 trials of checkpoint inhibitors for people with squamous cell carcinoma of the head and neck (HNSCC).

Table 6.20 Results from the Checkmate‐141 involving 361 people with metastatic or recurrent HNSCC whose cancer had progressed within six months of receiving platinum‐based chemotherapy.

Table 6.21 Results from the IMvigor 210 and IMvigor 211 clinical trials investigating atezolizumab/Tecentriq for people with invasive bladder cancer, who had previously been treated with platinum‐based chemotherapy.

Table 6.22 Phase 3 trials of checkpoint inhibitors in bladder cancer, as of December 2017.

Chapter 07

Table 7.1 Summary of some of the most common hematological cancers diagnosed in the United Kingdom.

Table 7.2 The cell of origin of various hematological cancers.

Table 7.3 Some common translocations found in hematological cancer cells.

Table 7.4 Targeted treatments licensed for people with hematological cancers, as of December 2017.

Table 7.5 BCR signaling in various B cell cancers.

Table 7.6 Bcr‐Abl inhibitors licensed for use in the United States and United Kingdom.

List of Illustrations

Chapter 01

Figure 1.1

A chromosome translocation.

Two chromosomes (colored turquoise and orange) break. The cell accidentally sticks them back together incorrectly. If the chromosomes have broken where genes are located, this may result in the creation of a gene fusion.

Figure 1.2

The TMPRSS2 ‐ ERG gene fusion found in prostate cancer cells

.

(a)

In healthy prostate cells, androgen receptors pair up due to the presence of testosterone. Paired‐up receptors then attach to the TMPRSS2 gene promoter and cause the cell to produce TMPRSS2 protein.

(b)

In contrast, prostate cells only rarely produce ERG, because the ERG gene does not contain attachment sites for androgen receptors.

(c)

50% of prostate cancers contain a chromosome rearrangement which puts the protein‐coding region of the ERG gene under the control of the promoter from the TMPRSS2 gene. This mutation causes the cell to produce ERG, which in turn forces the cell to multiply.

Figure 1.3

A chromosome insertion

– part of one chromosome is inserted into another chromosome (as shown) or back into the same chromosome but in the wrong location.

Figure 1.4

Chromosome deletions and inversions. (a)

In a chromosome deletion, part of a chromosome is (not surprisingly) deleted. An example is the deletion of part of chromosome 17 containing the

TP53

gene in chronic lymphocytic leukemia, bowel cancer, and other cancers.

(b) Chromosome inversion

– a segment of the chromosome is cut out, flipped over, and inserted back into the chromosome; for example, inversions involving the

ALK

gene on chromosome 2 in lung cancer.

Figure 1.5

Gene amplification.

The cell accidently makes extra copies of part of a chromosome. The duplicate segments are inserted into other chromosomes or back into the same chromosome; for example, amplification of a segment of chromosome 17 containing the

HER2

gene in breast cancer.

Figure 1.6

Point mutations.

A point mutation (shown by a red star) is when one DNA base is added, deleted, or swapped for a different one in the cell’s DNA

(a)

. If the mutation is in a gene, the mutation will be copied into the mRNA

(b)

and it may alter the resulting protein. The consequence might be that

(c)

due to a

missense mutation,

the protein made by the cell differs from the normal (the so‐called “wild‐type”) version of the protein by one amino acid,

(d) a nonsense mutation in

the DNA introduces a stop signal into the mRNA, and the cell makes an extra‐short (truncated) protein,

(e)

a

silent mutation

has no impact on the protein produced,

(f)

a

frameshift

mutation causes the cell to make a very different protein compared to the normal protein, one which is only partly the same as the original.

Figure 1.7

The series of mutations leading to many bowel cancers. (a)

Orderly, well‐connected cells line the bowel.

(b)

A random mutation in a bowel cell lead to loss of APC activity; this cell starts to multiply slightly faster than its neighbors, forming a little lump – an adenoma. The faulty cells are not yet cancer cells, but because they are multiplying more quickly than normal, they are prone to collecting more mutations.

(c)

Weeks, months, or years later, a mutation in the

KRAS

gene causes the K‐Ras protein to become overactive; the cells now multiply rapidly and in a disorderly fashion.

(d)

Finally, genes like

TP53

,

PIK3CA

, and

SMAD4

are mutated. The faulty cells are now full‐blown cancer cells, able to invade through local tissues and spread to other parts of the body.

Abbreviations:

APC

– adenomatous polyposis coli;

TP53

– tumor protein 53;

PIK3CA

‐phosphatidylinositol‐4,5‐bisphosphate 3‐kinase catalytic subunit alpha;

SMAD4

– SMAD family member 4

Figure 1.8

Genome instability drives intratumoral heterogeneity. (a)

In a microscopic cluster of cancer cells, all the cells are likely to contain the same genetic faults. However, the cells are

genomically unstable

and likely to pick up more mutations.

(b)

The cells start to evolve and become different from one another.

(c)

As time goes on, the cells diverge from each other more and more, creating distinct populations of cells driven by different sets of mutations.

Figure 1.9

The cancer microenvironment contains many different types of cells

. Tumors contain cancer cells, many different types of white blood cells, fibroblasts, fat cells (adipocytes) and other cell types (not shown). Winding their way through them are blood vessels, which are made up of endothelial cells and pericytes. Lymph vessels might also be present (not shown). All of these proteins are embedded in a protein scaffold called the extracellular matrix (ECM).

Figure 1.10

Cancer angiogenesis. (a)

A cluster of cancer cells is too far away from the nearest blood vessel to receive an adequate blood supply.

(b)

The drop in oxygen levels triggers the cancer cells to release VEGF into their surroundings.

(c)

VEGF attaches to VEGF receptors on the surface endothelial cells, causing the blood vessel to sprout and grow.

(d)

The tumor contains a convoluted, lumpy, leaky network of blood vessels; many cancer cells now have sufficient blood supply, but many others do not.

Abbreviations:

VEGF – vascular endothelial growth factor

Figure 1.11

The path to metastasis. (a)

A primary tumor containing many different cell types.

(b)

A cancer cell that is particularly mobile might invade locally and squeeze its way into blood vessels.

(c)

A cancer cell circulating in the blood.

(d)

The cancer cell squeezes out of the blood vessel into a new environment.

(e)

In its new location, the cancer cell may die or remain dormant for weeks or even years, kept in check by its new environment. However, eventually a change in its environment or the gain of new mutations might enable it to multiply and create a metastasis.

Figure 1.12

The epithelial‐to‐mesenchymal transition ( EMT ). (a)

All our body’s organs and tissues are lined with epithelial cells. Epithelial cells tend to be lined‐up and well connected to one another. They are also physically attached to the basement membrane.

(b)

During the EMT, cells gradually lose epithelial proteins and gain mesenchymal proteins.

(c)

Mesenchymal cells are mobile and resilient and less well connected to one another and the basement membrane.

Abbreviations:

EMT – epithelial‐to‐mesenchymal transition; MET – mesenchymal to epithelial transition

Figure 1.13

Intratumoral heterogeneity is an obstacle to effective cancer treatment.

Due to the genomic instability of cancer cells, cancers often contain multiple populations of cancer cells driven by different combinations of mutations (represented by the different colors).

(a)

A biopsy sample (illustrated by the dotted red circle) does not contain representative cells from the whole cancer and may give scientists a skewed view of what mutations are driving the cells’ behavior.

(b)

Some cancer cells are killed by a treatment (red crosses).

(c)

However, many other cells contain mutations that make them resistant and able to survive.

(d)

A cancer cell that leaves the original tumor and creates a metastasis elsewhere in the body may have very different properties from the original tumor.

Figure 1.14

The pancreatic cancer microenvironment can protect cancer cells from the effects of treatment. (a)

Pancreatic cancers often contain a dense, fibrous network of proteins that compresses any blood vessels that are present and prevents cancer drugs from penetrating the tumor.

(b)

Stellate cells (modified fibroblasts) produce fibrous proteins and release pro‐survival proteins such as growth factors.

(c)

White blood cells secrete many small proteins and chemicals that protect cancer cells from treatments.

Chapter 02

Figure 2.1

A very brief history of some important milestones in the development of non‐surgical cancer treatments.

The timeline includes milestones in radiotherapy [1], chemotherapy [2], hormone therapy for prostate cancer [3] and breast cancer [4], monoclonal antibody therapies [5], kinase inhibitors [6], and immunotherapies [7].

Figure 2.2

Some of the targets of targeted cancer treatments. (a)

Cancer cells often overproduce proteins called growth factor receptors, which are found on the cells’ surface and are hence accessible to monoclonal antibodies. Sometimes these growth factor receptors are faulty and overactive. (

b

) Growth factor receptors trigger the activity of other proteins inside the cell, many of which are kinases that can be blocked with kinase inhibitors.

(c)

Blood cell cancers (e.g., leukemias and lymphomas) have many proteins on their surface known as CD antigens. Many CD antigens (e.g., CD20, CD38, and CD19) are the targets of antibody‐based treatments for blood cancers.

(d)

Tumors need a blood supply, hence they produce signaling proteins that trigger the growth of blood vessels by a process called angiogenesis. These signaling proteins are blocked by a group of treatments known as the angiogenesis inhibitors.

(e)

Some cancers are driven by hormones such as estrogen (breast cancer) or testosterone (prostate cancer). The production of these hormones, or their actions, can be blocked using hormone therapies.

(f)

Some cancers contain fusion proteins. If these fusion proteins are kinases (e.g., Bcr‐Abl) they can be blocked with kinase inhibitors.

(g)

Our cells use proteasomes to recycle old and unwanted proteins. Some cancer cells seem dependent on proteasomes for their survival and can be treated with proteasome inhibitors.

(h)

Many cancers have difficulty repairing DNA damage; this vulnerability can be exploited with treatments such as PARP inhibitors.

(i)

Many cancer cells have proteins on their surface such as PD‐L1 that directly suppress white blood cells. Cancer cells also persuade other cells in their surroundings to produce the same proteins; hence, they avoid being destroyed by the person’s immune system. Immunotherapies called checkpoint inhibitors can overcome this suppression.

(j)

Some antibody‐based treatments attach to cell surface proteins and deliver chemotherapy or other toxic substances.

(k)

Cancer cells often contain high levels of proteins such as Bcl‐2 that prevent the cell from undergoing apoptosis. Drugs that target Bcl‐2 or another of these proteins can force cancer cells to die.

Figure 2.3

Antibodies are made by specialized B cells. (a)

Our bodies contain many millions of white blood cells known as B cells, each of which has thousands of copies of a unique B cell receptor (BCR) on its surface.

(b)

B cells use their BCRs to recognize and connect with proteins and other complex molecules on the surface of invading pathogens such as bacteria and viruses. Anything that a BCR can connect with is known as an antigen.

(c)

When a B cell’s BCRs connect with an antigen, they are activated. After numerous further activation steps, the B cell may become a plasma cell and release millions of copies of its BCR into the blood. BCRs released into the blood are known as antibodies or immunoglobulins.

Figure 2.4 Antibodies are large proteins put together in a particular way. Each antibody contains four separate proteins: two

heavy chain

proteins and two

light chain

proteins. These four proteins are held together by chemical bonds (shown in dark red). Each B cell makes an antibody with a unique antigen‐binding region, which is created from the ends of the heavy and light chains. Because the antigen‐binding regions vary, they are called the “variable region” of the antibody.

Figure 2.5

Antibodies can block growth factor receptors in several different ways.

Many of the proteins targeted by monoclonal antibody treatments are growth factor receptors; these are complicated proteins that attach to growth factors and activate signaling proteins within the cell. Antibodies can block growth factor receptors by:

(a)

attaching to growth factor receptors and preventing growth factors from gaining access;

(b)

directly blocking the receptor’s activity;

(c)

preventing receptors from pairing up (receptors are only active when in pairs);

(d)

attaching directly to the growth factor and preventing it from binding to its receptor. Blocking the growth factor receptors on the surface of cancer cells is sometimes sufficient to kill them.

Figure 2.6

Antibodies can kill cancer cells by attracting white blood cells and complement proteins

. When an antibody attaches to a protein on a cancer cell, it can attract white blood cells such as macrophages and natural killer (NK) cells.

(a)

Macrophages can engulf and digest cancer cells through phagocytosis.

(b)

NK cells release cell‐killing enzymes that lyse (destroy) the cell. Together these mechanisms are called “antibody‐dependent cell cytotoxicity” (ADCC).

(c)

Antibodies attached to cancer cells also attract complement proteins that come together to form a membrane attack complex (MAC) that can punch holes through the cell’s membrane and kill the cell. This is called “complement‐dependent cytotoxicity” (CDC).

Figure 2.7

Different types of antibodies used as cancer treatments.

The scientific name (i.e., not the marketing name) of monoclonal antibodies always ends in

mab

to denote it as a monoclonal antibody. Letters within the name tell you whether it is a mouse antibody (

o

), a chimeric (part mouse, part human) antibody (

xi

), a humanized (almost completely human) antibody (

zu

), or a fully human antibody (

u

). The letters “li” or just “l” in pembrolizumab, atezolizumab, nivolumab, and durvalumab denote that these are immunotherapies that target the immune system.

Figure 2.8

An antibody’s effectiveness can be improved by tweaking its structure.

Some antibodies have been improved upon by making slight changes to the antibody’s antigen‐binding site. Other modifications include altering the constant region of the antibody (either by changing the amino acid sequence or adding sugar molecules) to improve the antibody’s ability to attract white blood cells and complement proteins.

Figure 2.9

Mechanism of action of antibody–drug conjugates ( ADCs ). (a)

ADCs are made from an antibody, a linker, and one or more molecules of a chemotherapy. Two commonly used chemotherapies are calicheamicin and auristatins.

(b)

An ADC attaches to its target protein on the surface of a cell.

(c)

The cell’s membrane folds inward to create a compartment (an endosome) containing the ADC.

(d)

The ADC’s linker is broken, releasing toxic chemotherapy.

(e)

The chemotherapy is released into the cell cytoplasm, where it kills the cell by destroying its microtubules (auristatins) or by causing DNA breaks (calicheamicin).

(f)

The antibody’s target protein may be destroyed or recycled back to the cell surface.

Figure 2.10

A bi‐specific antibody

. The antibody is constructed from the variable regions of an anti‐CD19 antibody and an anti‐CD3 antibody, which are held together by a linker. The bi‐specific antibody draws together a CD19‐expressing B cell with a CD3‐expressing T cell.

Figure 2.11

The structure of ATP.

ATP is made from adenine, a sugar molecule called ribose, and three phosphates. The bonds holding together the phosphates release lots of energy when they are broken. When ATP loses one of its phosphates, it becomes a lower‐energy molecule called ADP. When it loses two phosphates, it becomes AMP. As well as making up part of the ATP molecule, adenine is also found in DNA and RNA.

Abbreviations:

ATP – adenosine tri‐phosphate; ADP – adenosine di‐phosphate; AMP – adenosine mono‐phosphate

Figure 2.12

Kinases are catalysts that attach phosphates to other proteins and molecules in our cells. (a)

Kinases have docking sites for both ATP and one or more substrates (in this case, an inactive protein).

(b)

Both ATP and the inactive protein dock with the kinase.

(c)

The kinase transfers one of the phosphates from ATP to a tyrosine, threonine, or serine amino acid in the protein. This activates the protein. What was ATP is now ADP. The active protein and ADP are released by the kinase.

Abbreviations:

ATP – adenosine tri‐phosphate; ADP – adenosine di‐phosphate

Figure 2.13

Growth factor receptors are kinases.

Growth factor receptors are large proteins that sit in our cells’ outer membrane. They have three main parts: an extracellular domain that sticks outside the cell, a transmembrane domain that spans the cell membrane, and an intracellular domain that protrudes into the cell cytoplasm. The intracellular domain has two important features: a docking site for ATP and multiple tyrosine (Y) amino acids. When ATP slots into its docking sites, the growth factor receptors phosphorylate each other on tyrosine amino acids. Growth factor receptors become active when phosphorylated.

Abbreviations:

ATP – adenosine tri‐phosphate

Figure 2.14

Most kinase inhibitors work by mimicking the shape of ATP

.

(a)

All kinases have a binding site for ATP. When the kinase is activated, the ATP‐binding site becomes accessible and ATP enters. The kinase is then able to phosphorylate its targets.

(b)

Kinases can be blocked by drugs that mimic the shape of ATP and that compete with ATP for the kinase’s ATP‐binding site.

(c)

In a cancer cell that is resistant to treatment with a kinase inhibitor, the gene for the target kinase has often sustained a mutation that has changed the binding site’s shape. The mutation means that ATP can still enter its binding site, but the drug cannot; therefore, the kinase remains active, and the cancer cell survives.

Abbreviations:

ATP – adenosine tri‐phosphate

Figure 2.15

There are four classes of kinase inhibitors, and drugs that block kinases indirectly. (a)

Type 1 kinase inhibitors compete with ATP for the ATP‐docking site of active kinases.

(b)

Type 2 kinase inhibitors can enter a kinase’s ATP‐binding site only when the kinase is inactive. The ATP‐binding site of inactive kinases contains an extra pocket created by the kinase’s activation loop.

(c)

Allosteric inhibitors bind outside of the ATP‐binding site.

(d)

Covalent inhibitors enter the kinase’s ATP‐binding site and form chemical bonds that hold the drug in place.

(e)

Indirect kinase inhibitors do not bind to the kinase directly; instead, they attach to a separate protein that only inhibits the kinase when the drug is present.

Abbreviations:

ATP – adenosine tri‐phosphate

Figure 2.16

The idea behind synthetic lethality

.

(a)

In healthy cells, K‐Ras is normal, and CDK enzymes are not overactive. Blocking CDKs should have little impact on the cells.

(b)

In many cancer cells, K‐Ras is faulty and overactive, and this in turn forces the cells’ CDK enzymes to be overactive. The combination (synthesis) of faulty K‐Ras plus a CDK inhibitor is lethal to the cancer cells.

Abbreviations:

CDK – cyclin‐dependent kinase

Chapter 03

Figure 3.1

Our cells respond to a wide range of short‐range and long‐range signals

. Short‐range signals include growth factors, which travel short distances between cells. Our cells also respond to oxygen and nutrients, to complex proteins and sugars in their immediate surroundings (called the extracellular matrix), and to physical contact with neighboring cells. Long‐range signals that cells respond to include hormones, which are produced and released by specialized glands throughout the body, such as the adrenal glands, the hypothalamus and pituitary gland in the brain, the testes (in men), and ovaries (in women). Hormones travel throughout the body and affect distant cells. White blood cells that live in the bone marrow and lymphoid tissues, or that patrol the body and accumulate at the site of infections and injuries, send out a wide variety of signals in the form of tiny proteins such as cytokines and chemokines. Finally, specialized cells such as nerve cells (neurons), ear cells, eye cells, and other sensory cells respond to signals such as neurotransmitters, sound, light, and touch.

Figure 3.2

Activation of growth factor receptors keeps our cells alive

.

(a)

Cells produce and release growth factors into their surroundings.

(b)

Growth factors attach to growth factor receptors and cause them to pair up. This pairing up activates the receptors’ kinase domain, and they phosphorylate one another; paired‐up receptors activate other proteins in the cell.

(c)

The activated proteins go on to activate more proteins, and more proteins, and this transmits the signal through the cell’s cytoplasm (shown with a dotted black line). Eventually, the signal reaches the nucleus.

Figure 3.3

Growth factors can have a variety of different impacts on cells

.

(a)

Healthy cells need growth factors to stay alive.

(b)

Changes to the amount and type of growth factors present gives this healthy cell a signal to grow and multiply.

(c)

Mutations in cancer cells’ DNA, and changes to the amount of growth factors and growth factor receptors on their surface, provide cancer cells with continuous signals to survive, cause them to multiply, increase their mobility, alter their metabolism, and trigger angiogenesis.

Figure 3.4

Growth factor receptors phosphorylate one another when growth factors attach to them

.

(a)

An unpaired EGFR.

(b)

When growth factors such as EGF attach to EGFRs, the receptors change shape, thus exposing their interaction domains; they then pair up (dimerize).

(c)

The paired receptors phosphorylate each other.

(d)

The addition of phosphates creates docking sites for other proteins.

Figure 3.5

Some of the many proteins and pathways activated by growth factor receptors

[10–12]. When growth factor receptors pair up, they activate many different signaling proteins in the cell, which control processes such as proliferation, survival, growth, and the cell’s ability to move. Some of the most important and well‐known signaling pathways are those that involve Ras, Raf, MEK, and ERK (known as the MAPK pathway), and PI3K, AKT, and mTOR. This latter pathway is kept under control by PTEN, which prevents the activation of AKT. Rac and Rho control the cell’s internal skeleton. ERK, PKC, and mTOR have numerous effects on the cell, including forcing it into cell cycle and enabling it to grow. NFκB is a powerful transcription factor that, once in the nucleus, prevents cell death. STAT is also a transcription factor. As well as being activated by JAK, it is also directly activated by some growth factor receptors. When activated, STAT proteins pair up and enter the nucleus.

Abbreviations:

STAT – signal transducer and activator of transcription; mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK‐ extracellular‐signal‐regulated kinase; PLC – phospholipase C; PKC – protein kinase C; NFκB – nuclear factor kappa‐B; JAK – Janus kinase; PTEN – phosphatase and tensin homologue

Figure 3.6

All four EGF receptors can pair up with one another to create homo‐ and heterodimers.

A homodimer is when two identical receptors have paired up. A heterodimer contains two different receptors. HER2 is different from HER1, HER3, and HER4 in that it doesn’t need a growth factor to be present in order for it to pair up.

Abbreviations:

HER – human epidermal growth factor receptor; EGF – epidermal growth factor

Figure 3.7

Signaling pathways are overactive in cancer cells for a variety of reasons

.

(a)

Some cancers produce vast amounts of growth factors that saturate all the available receptors.

(b)

Cancer cells also overproduce growth factor receptors and become hypersensitive to the presence of growth factors.

(c)

The overproduced receptor is often faulty and overactive, sometimes even in the absence of any growth factors.

(d)

Proteins inside the cell that pass on the growth signal are mutated and overactive, for example, Ras (K‐Ras, N‐Ras, and H‐Ras), B‐Raf, PI3K, and AKT; proteins that would normally block the pathway (e.g., PTEN) are missing.

(e)

The signaling pathway is constantly active, and this forces the cell to constantly grow and multiply and makes it insensitive to DNA damage.

Figure 3.8

Numerous treatments target either EGFR or HER2

. Monoclonal antibodies attach to the external part of the receptors. Kinase inhibitors cross the cell membrane and block the kinase part of the receptors. Many kinase inhibitors have more than one target, and the pan‐HER inhibitors block EGFR, HER2 and HER4 or EGFR, HER2 and HER3.

Abbreviations:

EGFR – epidermal growth factor receptor; HER2 – human epidermal growth factor receptor‐2; VEGF – vascular endothelial growth factor

Figure 3.9

Comparison of panitumumab and cetuximab.

Both treatments are monoclonal antibodies. However, cetuximab is chimeric – the back part of the antibody is a human IgG1 antibody, whereas the antigen‐binding region is from a mouse antibody. Panitumumab is a fully human IgG2κ antibody.

Figure 3.10

Mutations affecting the MAPK pathway and PI3K pathway cause intrinsic resistance to EGFR ‐targeted antibodies

. Bowel cancer cells often contain mutated, overactive versions of Ras (particularly K‐Ras), Raf (generally B‐Raf), or PI3K (mutated proteins are shown as spiky ovals). The presence of any of these mutated proteins causes overactivity of the MAPK pathway (Ras/Raf/MEK/ERK) and the PI3K pathway (PI3K/AKT/mTOR). And, when these pathways are overactive, the receptor on the cell surface becomes redundant. Blocking the activation of EGF receptors using an EGFR‐targeted antibody will then have no impact on the cell and will bring no benefit for the patient.

Abbreviations:

EGFR – epidermal growth factor receptor; mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK‐ extracellular‐signal‐regulated kinase; PTEN – phosphatase and tensin homologue

Figure 3.11

Reasons for resistance to EGFR ‐targeted kinase inhibitors in NSCLC cells

. Resistance mechanisms include

(a)

Cancer cells have gained an additional mutation, the T790M mutation, in the EGFR gene, which has altered the ATP‐binding site of EGFR such that the drug can no longer block it.

(b)

Cancer cells have additional growth factor receptors on their surface such as HER2, MET, or FGFR.

(c and d)

Cancer cells contain mutated overactive B‐Raf or PI3K.

(e)

Cells have lost NF1, which would normally block Ras proteins.

Abbreviations:

EGFR – epidermal growth factor receptor; mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK‐ extracellular‐signal‐regulated kinase; PTEN – phosphatase and tensin homologue; ATP – adenosine triphosphate; HER2 – human epidermal growth factor receptor‐2; FGFR –fibroblast growth factor receptor; NF1 ‐ neurofibromatosis type 1

Figure 3.12

Mechanism of action of HER2 ‐targeted antibodies

.

(a)

Trastuzumab attaches to HER2 near the cell membrane. It prevents paired‐up HER2 from activating signaling pathways. It also attracts white blood cells and prevents HER2 shedding.

(b)

Pertuzumab prevents HER2 from pairing up with EGFR or HER3, and thereby prevents the activation of signaling pathways (unpaired growth factor receptors cannot activate signaling pathways). Pertuzumab can also attract white blood cells.

(c)

Trastuzumab emtansine (T‐DM1) attaches to HER2 and becomes internalized within the cell. The chemotherapy part of T‐DM1 then breaks away and attacks the cell’s microtubules. T‐DM1 can also block signaling pathway activation and attract white blood cells just like the naked trastuzumab antibody.

Abbreviations:

EGFR – epidermal growth factor receptor; HER2 – human epidermal growth factor receptor‐2; HER3 – human epidermal growth factor receptor‐3

Figure 3.13

HER2 ‐positive cancers have extra copies of the HER2 gene

.

(a)

Normal cells have two copies of the

HER2

gene and produce very little HER2 protein.

(b)

HER2

gene amplification leads to overproduction of HER2, which pairs up with itself and other HER‐family receptors (namely, EGFR, HER3, and HER4). This causes increased activity of signaling pathways and promotes cell proliferation and survival.

Abbreviations:

EGFR – epidermal growth factor receptor; HER2 – human epidermal growth factor receptor‐2; HER3 – human epidermal growth factor receptor‐3; HER4 – human epidermal growth factor receptor‐4

Figure 3.14

Some reasons for resistance to HER2 ‐targeted antibodies in breast cancer cells. (a)

In cells sensitive to trastuzumab, the antibody is able to attach to HER2 and prevent it from activating signaling pathways.

(b)

Some trastuzumab‐resistant cells have mutations affecting the HER2 gene. They therefore manufacture overactive HER2, or HER2 that lacks a binding site for trastuzumab.

(c)

Another cause of resistance is the presence of other growth factor receptors on the cell surface.

(d)

Mutations affecting the PI3K pathway, such as those that cause PI3K to be overactive, or loss of PTEN, can also cause resistance.

Abbreviations:

mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK‐ extracellular‐signal‐regulated kinase; PTEN – phosphatase and tensin homologue; HER2 – human epidermal growth factor receptor‐2

Figure 3.15

Ras, Raf, MEK , and ERK activation. (a)

Paired‐up growth factor receptors phosphorylate one another, which allows a series of docking proteins to attach.

(b)

These docking proteins activate Ras (K‐Ras, N‐Ras, or H‐Ras) by causing it to let go of GDP (orange circle) and take hold of GTP (yellow circle) instead. Ras is constantly in contact with the cell membrane.

(c)

Ras attracts Raf proteins to the cell membrane where they pair up and become active. Raf proteins are kinases; they phosphorylate MEK, which in turn phosphorylates ERK.

Abbreviations:

GDP – guanosine di‐phosphate; GTP – guanosine triphosphate

Figure 3.16

The Raf inhibitor paradox

.

(a)

In healthy cells most Raf proteins exist as unpaired monomers that cannot activate MEK. The addition of a Raf inhibitor such as vemurafenib or dabrafenib therefore has little impact.

(b)

In cancer cells in which the B‐Raf protein is mutated and overactive, the faulty B‐Raf protein strongly activates MEK even as a monomer, which forces the cancer cell to grow and multiply.

(c)

Mutated B‐Raf monomers are blocked by the B‐Raf inhibitor, causing cell death.

(d)

Non‐cancer cells occasionally contain mutated, overactive versions of Ras proteins, such as N‐Ras. These faulty Ras proteins activate the cell’s Raf proteins, causing them to pair up and form dimers that activate MEK.

(e)

Treatment of these cells with a B‐Raf inhibitor actually activates the Raf dimers and causes even greater MEK activity, potentially causing a secondary cancer.

Figure 3.17

Some reasons for resistance to B‐Raf inhibitors in malignant melanoma cells

.

(a)

A B‐Raf inhibitor blocks mutated B‐Raf in a cancer cell.

(b)

Faulty, overactive versions of N‐Ras, C‐Raf, PI3K, and AKT can activate signaling pathways strongly enough that the cell survives.

(c)

Overproduction of C‐Raf reactivates MEK despite B‐Raf inhibition.

(d)

Extra mutations in the

BRAF

gene cause the cell to manufacture a shortened (truncated) version of B‐Raf that cannot be blocked.

(e)

Cancer cells that have high levels of growth factor receptors on their surface can activate C‐Raf and the PI3K/AKT/mTOR pathway to such a degree it can survive B‐Raf inhibition.

(f)

Amplification of the mutated

BRAF

gene causes massive production of mutated B‐Raf protein, which overwhelms the drug.

Abbreviations:

mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK‐ extracellular‐signal‐regulated kinase; PTEN – phosphatase and tensin homologue

Figure 3.18

The basics of the PI3K / AKT / mTOR signaling pathway

.

(a)

As with the MAPK pathway, the PI3K/AKT/mTOR pathway can be triggered by paired‐up growth factor receptors that phosphorylate one another (shown by the red circles).

(b)

The paired‐up receptors activate P13K, which indirectly activates AKT.

(c)

AKT has numerous impacts on the cell, including triggering cell proliferation, survival, and altered metabolism.

(d)

AKT also activates mTOR, an important controller of cell growth, motility, and angiogenesis.

(e)

mTOR is active when it comes together with other proteins to form mTOR complex‐1 (mTORC1) and mTOR complex‐2 (mTORC2). mTORC1 and mTORC2 have distinct, but overlapping, effects on the cell.

(f)

mTORC2 also causes further activation of AKT.

(g)

In addition, mTORC is influenced by proteins that respond to the cell’s well‐being and environment, such as changing levels of glucose, amino acids, ATP, and oxygen.

Abbreviations:

mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK‐ extracellular‐signal‐regulated kinase; PTEN – phosphatase and tensin homologue; ATP – adenosine triphosphate

Figure 3.19

PI3K comes in various different forms

. There are numerous versions of the two subunits that come together to create PI3K [80]. Each subunit is encoded by a different gene.

(a)

The most commonly‐mutated gene for a PI3K subunit in cancer cells is

PIK3CA

, which is the gene for making the p110‐alpha subunit of PI3K‐alpha. A wide variety of mutations in

PIK3CA

have been found in numerous solid tumors.

(b)

PI3K‐beta has overlapping roles with PI3K‐alpha and seems to be particularly important to cancer cells that have lost PTEN, which includes the majority of prostate cancers.

(c)

PI3K‐delta is predominantly found in white blood cells, in which it is activated by B cell receptors.

(d)

PI3K‐gamma is activated by G‐protein‐coupled receptors rather than by growth factor receptors.

Abbreviations:

PI3K – phosphatidylinositol 3‐kinase; PTEN – phosphatase and tensin homologue

Figure 3.20

The basics of the JAK ‐ STAT signaling pathway. (a)

JAK is activated when two or more cytokine receptors come together due to the presence of a ligand, such as a cytokine, growth factor, or hormone.

(b)

JAK phosphorylates STAT transcription factors, which are in the cytoplasm.

(c)

The phosphorylated STATs pair up and move into the nucleus. In the nucleus, STATs control the production of a variety of proteins that together encourage the cell to multiply.

(d)

ERK adds to STAT activity by attaching further phosphates.

(e)

JAK directly activates PI3K and indirectly activates Ras, triggering MAPK pathway and PI3K/AKT/mTOR pathway activity.

Abbreviations:

JAK – janus kinase; STAT – signal transducer and activator of transcription; mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK‐ extracellular‐signal‐regulated kinase

Chapter 04

Figure 4.1

Why block VEGF ?

This table lists the various properties of VEGF, VEGF receptors, and VEGF signaling pathways, and explains why VEGF and VEGF receptors are the target of the vast majority of angiogenesis inhibitors.

Abbreviations:

VEGF – vascular endothelial growth factor

Figure 4.2

Longitudinal illustration of a cancer blood vessel.

Healthy blood vessels are lined by endothelial cells, which should create an orderly, continuous layer. In a tumor blood vessel, the endothelial cells are less orderly, and there are gaps between them.

(a)

In places, cancer cells take the place of endothelial cells.

(b)

Integrins on the surface of endothelial cells connect with the basement membrane and with proteins in the extracellular matrix.

(c)

Binding of VEGF to its receptors activates the Ras/Raf/MEK/ERK pathway, PI3K/AKT/mTOR pathway, and other pathways.

(d)

The tumor microenvironment contains numerous cell types, including fibroblasts and white blood cells.

(e)

Pericytes provide support to endothelial cells and participate in angiogenesis.

Abbreviations:

VEGF – vascular endothelial growth factor; mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK – extracellular‐signal‐regulated kinase

Figure 4.3

Mechanism of action of various angiogenesis inhibitors. (a)

Bevacizumab, a humanized monoclonal antibody, attaches to VEGF‐A and keeps it away from VEGF receptors.

(b)

Aflibercept, a bioengineered protein, attaches to VEGF‐A, VEGF‐B and PlGF, keeping them away from VEGF receptors.

(c)

Ramucirumab is a humanized antibody that directly attaches to VEGF receptor 2.

(d)

Various kinase inhibitors block the kinase portion of VEGF receptors and of other growth factor receptors.

Abbreviations:

VEGF – vascular endothelial growth factor; PlGF – placental growth factor

Figure 4.4

Structure of aflibercept (ziv‐aflibercept; Zaltrap). (a)

Aflibercept is made from parts taken from three separate proteins: VEGFR1, VEGFR2, and an antibody. (

b)

Diagram showing which parts of VEGFR1 and VEGFR2 are incorporated into aflibercept.

Abbreviations:

VEGF – vascular endothelial growth factor; PlGF – placental growth factor; VEGFR – VEGF receptor

Figure 4.5

Basic mechanism of action of kinase inhibitors that block VEGF receptors. (a)

Kinase inhibitors easily enter cells by crossing the cell membrane. (

b)

They mimic the shape of ATP and compete for the receptor’s ATP‐binding site. This prevents paired‐up VEGF receptors from phosphorylating each other.

(c)

Without phosphates, there are no docking sites for other proteins, and hence the receptors cannot activate signaling pathways that would normally cause angiogenesis.

Abbreviations:

VEGF – vascular endothelial growth factor; ATP – adenosine tri‐phosphate

Figure 4.6

Reasons for resistance to angiogenesis inhibitors: rebound growth factor production and survival of hypoxia‐resistant cells. (a)

Angiogenesis inhibitors cause oxygen levels to drop, which triggers tumor cells and endothelial cells to produce even greater quantities of VEGF, PDGF, PlGF, angiopoitins, and other growth factors.

(b)

These growth factors activate receptors on endothelial cells, keeping them alive and triggering yet more angiogenesis.

(c)

Some cancer cells contain DNA mutations and other adaptations that enable them to survive low oxygen levels, making them insensitive to angiogenesis inhibitors.

Abbreviations:

VEGF – vascular endothelial growth factor; PDGF – platelet‐derived growth factor; PlGF – placental growth factor

Figure 4.7

Reasons for resistance to angiogenesis inhibitors: bone marrow cells, the EMT , and increased pericytes. (a)

Low oxygen levels and the presence of some growth factors attract cells from the bone marrow. These cells infiltrate the tumor and produce a variety of cytokines and growth factors that encourage more angiogenesis.

(b)

The drop in oxygen caused by angiogenesis inhibitors can trigger cancer cells to undergo the EMT, leading to increased cancer cell aggression and invasion into neighboring tissues.

(c)

Drug‐resistant tumors have greater numbers of pericytes supporting and stabilizing their blood vessels and reducing their requirement for VEGF.

Abbreviations:

VEGF – vascular endothelial growth factor; EMT – epithelial‐to‐mesenchymal transition

Figure 4.8

How fusion proteins are created. (a)

Each of the 46 chromosome in our cells contains hundreds of genes. Cancer cells often contain broken chromosomes, and sometimes two chromosomes have broken at the location two different genes (labeled A and B).

(b)

As the cell repairs the damage, it might accidently put the chromosomes together the wrong way round so that the two genes end up next to each other.

(c)

When the cell transcribes the fusion gene, it creates a strand of mRNA that contains information from both genes.

(d)

Ribosomes use the information in the mRNA to create a fusion protein.

Abbreviations:

mRNA – messenger RNA

Figure 4.9

Cancer‐causing mutations in the

ALK

gene

.

(a)

A translocation or other chromosome rearrangement involving the

ALK

gene forces the cell to make an uncontrollable ALK fusion protein.

(b)

A mutation affecting the kinase part of ALK has made it overactive.

(c)

Amplification (extra copies) of the

ALK

gene forces the cell to make extra ALK protein.

(d)

Overactivity of ALK triggers numerous signaling pathways (not all shown) which force the cell to grow, multiply, and stay alive.

Abbreviations:

ALK – anaplastic lymphoma kinase; EML4 – echinoderm microtubule associated protein‐like 4; mTOR – mammalian target of rapamycin; PI3K – phosphatidylinositol 3‐kinase; ERK – extracellular‐signal‐regulated kinase

Figure 4.10

The role of PARP and BRCA proteins in repairing DNA damage. (a)

Thousands of small nicks in our DNA occur every day. They are repaired through a process that relies on PARP proteins

. (b)

If left unrepaired, a single‐strand nick ultimately becomes a double‐strand break

. (c)

Using homologous recombination, which is dependent on both BRCA proteins, the cell accurately repairs the double‐strand break.

Abbreviations:

PARP – Poly(ADP‐ribose) polymerase; BRCA – breast cancer susceptibility gene

Figure 4.11

The path from BRCA mutations to cancer. (a)

If a woman is born with a fault in one of her

BRCA

genes, then every cell in her body will contain the fault. But the second, healthy copy of the gene is enough to keep her healthy.

(b)

If the second copy of the affected

BRCA

gene gets damaged in one of her breast or ovary cells, this cell will be completely unable perform homologous recombination. Instead, the cell will have to rely on an error‐prone method (called non‐homologous end joining – NHEJ) to repair double‐strand breaks to its DNA.

(c)

Because it has to rely on NHEJ, the cell is genomically unstable and accumulates damage to many important genes.

Abbreviations:

NHEJ – non‐homologous end joining; BRCA – breast cancer susceptibility gene

Figure 4.12

A PARP inhibitor does not kill cells with both PARP and BRCA proteins. (a)

The blue oval represents the nucleus of a healthy cell, in which you find both PARP and BRCA proteins (and all the other proteins necessary for DNA repair). This cell’s DNA is constantly getting damaged (represented by yellow spiky circles and broken orange DNA strands).

(b)

Single‐strand breaks are repaired by a PARP‐dependent process; double‐strand breaks are repaired using homologous recombination (HR).

(c)

Exposing the cell to a PARP inhibitor (red triangles) prevents it from repairing single‐strand breaks, which ultimately become double‐strand breaks. However, double‐strand breaks are repaired using HR, and the cell is fine.

Abbreviations:

PARP – Poly(ADP‐ribose) polymerase; HR – homologous recombination; BRCA – breast cancer susceptibility gene

Figure 4.13

A PARP inhibitor does kill cells that lack either BRCA1 or BRCA2 proteins

.

(a)

The orange oval represents the nucleus of a

cancer cell

in a woman who has inherited a

BRCA

gene mutation. This cell contains PARP, but it is completely missing either the BRCA1 or BRCA2 protein. The cell therefore cannot perform homologous recombination (HR). This has led the cell to become genomically unstable, which has ultimately caused it to become a cancer cell.

(b)

When the cancer cell sustains damage to its DNA, it is forced to repair the damage using PARP (to repair single‐strand breaks) or non‐homologous end joining (NHEJ) to repair double‐strand breaks.

(c)

If the woman is treated with a PARP inhibitor, this prevents her cells from using PARP to repair single‐strand breaks. These breaks ultimately become double‐strand breaks, which the cancer cell can only repair using an error‐prone method such as NHEJ. The cell quickly accumulates DNA damage to critical levels, and the cell dies. The rest of the cells in her body, which still retain a healthy copy of the

BRCA

gene, can perform sufficient HR to stay alive.

Abbreviations:

PARP – Poly(ADP‐ribose) polymerase; HR – homologous recombination; NHEJ – non‐homologous end joining; BRCA – breast cancer susceptibility gene

Figure 4.14

The synthetic‐lethal situation created by the combination of BRCA mutations and PARP inhibition. (a)

The non‐cancer cells in a person with a

BRCA

mutation can perform homologous recombination.

(b)

Even if PARP is blocked with a PARP inhibitor, these cells stay alive.

(c)

Cancer cells in which both copies of either

BRCA1

or

BRCA2

are faulty cannot perform homologous recombination and rely on non‐homologous end joining to repair double‐strand breaks in their DNA.

(d)

The combination (synthesis) of the lack of BRCA protein

plus

a PARP inhibitor is lethal to the cancer cells.

Abbreviations:

PARP – Poly(ADP‐ribose) polymerase; BRCA – breast cancer susceptibility gene

Figure 4.15

The basics of the hedgehog signaling pathway

.

(a)

In the absence of hedgehog proteins, the Patched receptor blocks the hedgehog pathway by suppressing Smoothened (another receptor).

(b)

However, when hedgehog (Hh) proteins attach to Patched, it no longer blocks Smoothened, and Smoothened becomes active.

(c)

Increased Smoothened activity indirectly leads to the activation of GLI transcription factors. These transcription factors attach to numerous genes and

(d)

switch on production of various proteins including cyclin D1, Myc, and Bcl‐2, which encourage the cell to survive and multiply.

Abbreviations:

Hh – hedgehog; GLI – glioma associated

Figure 4.16

Paracrine activation of hedgehog signaling in pancreatic cancer. (a)

Around 75% of pancreatic cancers produce hedgehog (Hh) proteins.

(b)

Hh proteins activate the Hh pathway in nearby stromal cells, such as fibroblasts

. (c)

GLI transcription factors are activated, causing stromal cells to release growth factors and cytokines.

(d)

Growth factors released by stromal cells cause angiogenesis and activation of white blood cells.

(e)

Growth factor receptors on the surface of prostate cancer cells are activated, leading to cancer growth, invasion, and metastasis.

Abbreviations:

Hh – Hedgehog; GLI – glioma associated

Figure 4.17

The cell cycle of a human cell

.

(a)

The first stage in the cell cycle is G1, when the cell grows bigger and duplicates many of its proteins and other contents.

(b)

In S phase, the cell copies all 46 of its chromosomes so that it now has a duplicate set.

(c)

In G2, the cell checks its new chromosomes for mistakes and prepares for mitosis.

(d)

In mitosis, the cell separates its duplicate sets of chromosomes using a protein structure called the spindle.

(e)

The cell finally splits to create two identical cells, each with a full set of chromosomes.

Figure 4.18

CDKs phosphorylate RB . (a)

In a cell that is not multiplying, RB and E2F sit together on the cell’s DNA.

(b)

When the cell receives a signal to enter the cell cycle, this activates its CDKs, which then phosphorylate RB (phosphates are depicted as red circles on stalks).

(c)

Once phosphorylated, RB can no longer hold onto E2F proteins, and it lets go.

(d)

Without RB, E2F proteins (which are transcription factors) activate the transcription of numerous genes, causing the cell to make proteins that force it to enter the cell cycle.

Abbreviations:

RB – retinoblastoma associated protein; CDK – cyclin‐dependent kinase

Figure 4.19

CDKs are controlled by cyclins and CDK inhibitors. (a)

When a cell receives a signal to enter the cell cycle (such as activation of the MAPK and PI3K/AKT/mTOR pathways by growth factors), this causes the cell to produce cyclin D. Cyclin D activates two CDKs: CDK4 and CDK6, which phosphorylate RB and cause the cell to enter the G1 phase of the cell cycle.

(b)

One of the consequences of RB phosphorylation (and the resulting activity of E2F) is that the cell produces two more cyclins, cyclin E and cyclin A, which activate CDK2. CDK2 adds further phosphates to RB, triggering the cell to enter S phase and duplicate its chromosomes.

(c)

When all the cell’s chromosomes have been copied and checked for mistakes, CDK1 becomes active due to the actions of cyclin A and cyclin B, and the cell enters mitosis.

(d)

Finally, once cyclin B has been destroyed, the cell can split in two.

(e)

If something goes wrong with the cell cycle, CDKs can be blocked by CDK inhibitors such as p16, p15, p18, p19, p21, and p27.

Abbreviations:

RB – retinoblastoma protein; CDK – cyclin‐dependent kinase

Figure 4.20

Reasons why CDKs are overactive and E2F proteins are therefore uncontrolled in cancer cells

.

(a)

Signaling pathways such as the MAPK and PI3K/AKT/mTOR pathways are overactive in the majority of cancers, leading to increased production of cyclin D.

(b)

Many cancers contain extra copies of the genes for cyclins or CDKs, leading to increased production of these proteins.

(c)

The majority of breast cancers contain estrogen receptors, which force the cell to produce high levels of cyclin D1.

(d)

Many cancers lack important CDK inhibitors such as p16.

(e)

In some cancers, RB is missing, meaning that there is nothing to block E2F activity.

Abbreviations:

MAPK – mitogen‐activated protein kinase; PI3K – phosphatidylinositol 3‐kinase; mTOR – mammalian target of rapamycin; RB – retinoblastoma protein; CDK – cyclin‐dependent kinase

Figure 4.21

Mechanism of action of CDK 4/6 inhibitors

.

(a)

Drugs that block CDK4 and CDK6 can prevent phosphorylation of RB.

(b)

In the absence of phosphorylation, E2F and RB stay together, and E2F is unable to trigger entry into the cell cycle.

(c)

However, if RB protein is missing from the cell, then a CDK4/6 inhibitor will have no impact. This is because there is no RB to prevent E2F activity.

Abbreviations:

RB – retinoblastoma protein; CDK – cyclin‐dependent kinase

Figure 4.22

Possible mechanisms of resistance to CDK4 /6 inhibitors. (a)

CDK4/6 inhibitors work by preventing CDK4 and CDK6 from phosphorylating RB

. (b)

However, if RB is not present, perhaps because both of the cell’s copies of the

RB1

gene are deleted or suppressed, then an CDK4/6 inhibitor will have no impact on the cell.

(c)

Equally, overproduction of E2F might overwhelm the available RB.

(d)

Resistance can also take place if the cell overproduces cyclin E or

(e)

if it lacks p21 or p27.

Abbreviations:

RB – retinoblastoma protein; CDK – cyclin‐dependent kinase

Chapter 05

Figure 5.1

Mechanism of action of various cancer immunotherapies. (a)

The majority of checkpoint inhibitors are monoclonal antibodies that attach to checkpoint proteins, or their ligands, on the surface of white blood cells (such as T cells) or cancer cells. By disrupting the interaction between the checkpoint protein and its ligand, the antibody increases the white blood cells’ activity.

(b)

Adoptive cell transfer requires T cells (or other white blood cells) to be purified from the patient’s blood. These are then modified in the laboratory and infused back into the patient, where they attack cancer cells.

(c)

Peptide and DNA vaccines are either small fragments (peptides) of proteins found on the surface of cancer cells, or the DNA for such a peptide. The DNA or peptide is injected into the skin or muscle, where it is picked up by an antigen‐presenting cell (APC). The APC (usually a dendritic cell) displays the peptide on its surface (it may first need to make the peptide from the injected DNA) and presents it to T cells in lymph nodes. After receiving instructions from APCs, T cells move into the tumor and attack cancer cells. Vaccines can also be made from dead cancer cells. These are again injected into the body, where APCs digest them and display peptides from them on their surface.

(d)

Bi‐specific antibodies are modified antibodies that create a physical link between cancer cells and T cells, triggering the cell‐killing activity of the T cell.

Abbreviations:

APC – antigen‐presenting cell

Figure 5.2

The role of white blood cells in promoting pancreatic cancer. Mast cells

secrete growth factors that promote angiogenesis and invasion. They also produce cytokines that prevent other white blood cells from attacking cancer cells.

Tumor‐associated macrophages

facilitate tumor growth and metastasis (particularly into lymph nodes).

Myeloid‐derived suppressor cells ( MDSC )

are immature white blood cells that actively suppress any anti‐cancer immune cells (e.g., cytotoxic T cells).

Regulatory T cells

suppress cytotoxic T cells. Their presence is associated with increased aggressiveness of the cancer. Other cells in the pancreatic cancer microenvironment include

stellate cells

and

fibroblasts

, which produce and secrete a wide range of fibrous proteins such as collagen and fribronectin [7].

Abbreviations:

MDSC – myeloid‐derived suppressor cell

Figure 5.3

Even cancer cells with few peptides on their surface can trigger an immune response. (a)

Healthy cells display a wide range of peptides on the surface in conjunction with MHC class 1 proteins. These peptides are representative of the proteins the cell is making.

(b)

Cancer cells hide from the immune system by displaying a limited number of peptides on their surface.

(c)

Debris from dead and dying cancer cells includes peptides from mutated proteins. These peptides are picked up by antigen‐presenting cells (APCs) known as dendritic cells, which ingest the peptides and then display them on their surface in conjunction with MHC class 1 and class 2 proteins.

(d)

Dendritic cells displaying cancer peptides move to lymph nodes, where they display the peptides to T cells.

(e)

Some T cells recognize the peptides displayed to them with their T cell receptors and mount an anti‐cancer immune response.

Abbreviations:

MHC – major histocompatibility complex

Figure 5.4

Some of the checkpoint proteins on the surface of T cells.

As well as having the T cell receptor (TCR) on their surface, T cells also produce a wide range of

(a)

activating and

(b)

inhibitory checkpoint proteins that fine‐tune their activity [11].

Abbreviations:

TCR – T cell receptor

Figure 5.5

Activation and suppression of T cell activity via CD28 and CTLA ‐4. (a)

Activation (+) of a cytotoxic T cell by a dendritic cell requires two signals: (1) the T cell receptor must interact with an antigen displayed to it by an antigen‐presenting cell such as a dendritic cell, and (2) the CD28 protein on the T cell must engage with B7.

(b)

The activity of cytotoxic T cells is suppressed (−) when inhibitory checkpoint proteins on its surface are triggered. In this instance, suppression is mediated by CTLA‐4, an inhibitory checkpoint protein found on active T cells, which, like CD28, interacts with B7.

(c)

CTLA‐4 is also found on the surface of regulatory T cells (Tregs). Interaction between B7 and CTLA‐4 on Tregs increases (+) their activity.

Abbreviations:

MHC – major histocompatibility complex; Treg – regulatory T cell; CTLA‐4 ‐ Cytotoxic T lymphocyte‐associated molecule‐4

Figure 5.6

Suppression of T cells via PD ‐1 ligands.

Once a cytotoxic T cell has been activated by dendritic cells in a lymph node, it moves out into the tissues.

(a)

In the body’s tissues (e.g., in a cancer or at the site of an infection), the T cell’s activity can be maintained by tissue macrophages that display peptides via their MHC class 1 and class 2 proteins. However, tissue macrophages also display PD‐L1 and PD‐L1, which attach to PD‐1 and shut down the T cell’s activity.

(b)

Cancer cells in solid tumors frequently have PD‐L1 on their surface, through which they can suppress T cells with PD‐1 on their surface.

Abbreviations:

PD‐1 – programmed cell death protein‐1; MHC – major histocompatibility complex

Figure 5.7

An image taken through a microscope of a sample from a bowel cancer.

Some of the tumor‐infiltrating lymphocytes have been highlighted in yellow boxes. The cells have been stained to make them show up more clearly.

Figure 5.8

Using TILs for cancer immunotherapy. (a)

A tumor (malignant melanoma) is surgically removed. It contains many different cell types including cancer cells, T cells, macrophages, and myeloid‐derived suppressor cells.

(b)

The tumor is split up into single cells or small fragments.

(c)

The cells or fragments are grown in separate containers in the presence of a cytokine called IL‐2 (interleukin 2), which encourages T cells to grow and multiply. Gradually, the T cells outgrow and outlast all other cell types.

(d)

Each population of T cells is tested for its ability to respond to peptides present on the patient’s cancer cells.

(e)

T cells that recognize and destroy cancer cells are encouraged to multiply.

(f)

The patient’s immune system is depleted with chemotherapy or radiotherapy. The T cells are then infused back into their bloodstream. Flask from: https://pixabay.com/en/flask‐beaker‐chemistry‐container‐309923/

Abbreviations:

IL‐2 – interleukin‐2

Figure 5.9

The basic premise of CAR adapted T cell therapy.

The goal of CAR T cell therapy is to treat the patient with genetically modified versions of their own T cells. First, T cells are collected from their blood. The gene for a CAR protein is then introduced into the T cell’s chromosomes, forcing the T cell to manufacture thousands of copies of the CAR protein and place them on its surface. The T cells are then given time to multiply. Once back in the patient’s body, the CAR protein enables the modified T cells to attach to target cells (hopefully cancer cells) and destroy them.

Abbreviations:

CAR – chimeric antigen receptor

Figure 5.10

Similarities between the BCR and TCR .

Both BCRs and TCRs have a constant region and a variable, antigen‐binding region. Neither BCRs nor TCRs protrude far inside the cell, nor are they kinases. CD79a and CD79b are needed to transmit signals from the BCR into the cell cytoplasm. CD3 does the same for TCRs.

Abbreviations:

BCR – B cell receptor; TCR – T cell receptor

Figure 5.11

Structure of a CAR (chimeric antigen receptor) protein.

CAR proteins are constructed from various pieces taken from a variety of different proteins. The extracellular, antigen‐binding region is the variable region (also called the scFv) of an antibody, which is held together by a linker – a short string of amino acids. This is joined to a spacer, which provides flexibility. This in turn is connected to a protein segment known as the transmembrane domain that spans the cell membrane. Inside the cell are stimulatory domains taken from a number of proteins such as CD3, CD28, OX40, or CD247. These protein segments powerfully trigger the activity of T cells.

Abbreviations:

CAR – chimeric antigen receptor

Figure 5.12

Viruses can be used to genetically modify T cells and force them to produce CAR proteins. (a)

A modified virus containing the gene for a CAR protein is used to genetically modify T cells taken from the patient’s blood. The CAR gene permanently integrates into the cells’ chromosomes.

(b)

T cells use the instructions in the CAR gene to manufacture the desired CAR protein. They insert this protein into their outer membrane.

Abbreviation:

CAR – chimeric antigen receptor

Figure 5.13

Bi‐specific antibodies

.

(a)

A genetically engineered, bi‐specific antibody tethers together a T cell with a cancer cell. One part of the bi‐specific antibody anchors it to CD19, while the other part attaches to CD3, which is part of the T cell receptor complex.

(b)