New Perspectives in Oncology Research

Cancer is the uncontrolled growth and spread of cells. There are many different types of cancers that affect any part of the body. According to the World Health Organization, lung, stomach, liver, colon and breast cancer cause most of the cancer deaths each year.

Tumours can be classified as follows:

• Carcinomas arise from the cells that cover external and internal body surfaces.
• Sarcomas are cancers arising from cells found in the supporting tissues of the body.
• Lymphomas arise in tissues of the body's immune system.
• Leukemias are cancers of the immature blood cells.

A variety of technical names to distinguish the many different types of cancers are used by physicians and scientists:

The transformation from a normal cell into a tumour cell is a multistage process, typically a progression from a pre-cancerous lesion to malignant tumours. The hallmark characteristics in tumour development are:

• Uncontrolled cell proliferation
• Loss of apoptosis
• Angiogenesis
• Tissue invasion and metastasis

Changes in tumoural cells are the result of the interaction between an individual's genetic factors and external agents, including physical, chemical and biological carcinogens. Ageing is also another fundamental factor for the development of cancer and tobacco use is the largest preventable cause of cancer in the world causing 22% of cancer deaths.

Taken from Bhatia and Sklar. Nat Rev Cancer 2002

Cancer cells often invade surrounding tissue and can metastasize to distant sites. Invasion refers to the direct migration and penetration by cancer cells into neighbouring tissues. Metastasis refers to the ability of cancer cells to penetrate into lymphatic and blood vessels, circulate through the bloodstream, and then invade normal tissues elsewhere in the body.

A significant proportion of cancers can be cured by a careful selection of one or more therapeutic approaches, such as surgery, radiotherapy, chemotherapy, and new treatments (targeted therapy: inhibitors of angiogenic factors, biological therapies or vaccines):

The tumor markers are substances produced by tumor cells and/or by other cells of the body in response to cancer. Some are related to a single type of cancer, although most of them are associated with two or more cancers. Biomarkers can be used with diagnostic aims, to detect cancer in early stages, as well as with therapeutic purposes, using them to plan an appropriate therapy regimen or for follow-up to evaluate the patient's response to treatment. However, so far no specific biomarker with enough sensitivity and specificity has been identified.

 

Emerging technologies provide the means by which new and single cancer biomarkers could be discovered:

A review of causes and treatment options for cancer can be observed in the following video:

1. Learn the hallmark characteristics of tumour development.
2. Familizarize yourself with the concept of tumour marker. 
3. Study the process of angiogenesis and metastasis as well as the main molecules involved.
4. Understand the concept of circulating tumour cells and minimal residual disease.
5. Be able to identify the main treatment approaches used in oncology.

Practical Session 3 – Group 2

The keys to this practical session can be found at this link.

Lorenzo's Oil (1992)

The movie Lorenzo's Oil is based on true events and is an extraordinarily useful material to think about the ethical issues raised regarding the treatment of adrenoleukodystrophy (ALD), for which there is no known therapy. In the following video, the disease and its symptoms are briefly explained:

Augusto Odone and Michaela Teresa Murphy Odone are Lorenzo's parents, the child affected by ALD and star of the film. Augusto and Michaela refused to accept the rapid fatal outcome of their child's illness and began a desperate seek for a treatment. After many hours of research and study, The Odones discovered an oil blend which slows the degenerative process of the disease. The treatment is called since then "Lorenzo's Oil". In recognition of the work of Augusto and Michaela, Augusto received an Honorary Doctorate from the University of Stirling (Stirling, Scotland, UK). In this tender picture we can see Lorenzo with his father, Augusto:

ALD treatment

1. Lorenzo’s oil with a diet low in very-long chain fatty acids (VLCFA). VLCFAs decrease in blood and prevents disease in a large number of cases. Its effectiveness is greatly reduced as the disease progresses.

2. Bone marrow transplantation. This treatment may be beneficial in patients with moderate neurological symptoms. It has been successful in children with early symptoms of cerebral demyelination.

3. Immunostimulatory therapy. The treatment involves applying high doses of intravenous immunoglobulins with dietary therapy. The results to date have not been very encouraging to stop the progression of the disease.

4. Immunosuppressive therapy. The aim of this treatment is to reduce inflammation of the white matter caused by the disease, which seems to be caused by pro-inflammatory cytokines. This inflammation appears to mediate the rapid progression of neurological symptoms. However, the treatment does not seem to stop the symptoms of the disease.

5. Statins. Statins are drugs that lower cholesterol levels. Its efficacy to stop the progress of the disease has been shown to be very limited.

6. Gene therapy. This therapy is intended to incorporate, by gene therapy, the gene encoding the protein ABCD1. In combination with bone marrow transplantation it represents the great hope for the treatment of patients with ALD.

 Image taken from Cartier et al. Hematopoietic Stem Cell Gene Therapy with a Lentiviral Vector in X-Linked Adrenoleukodystrophy. Science 2009;326:818-823.

Super Size Me (2004)

Many of the obesity-associated diseases are described in the film. Furthermore, we can see how some of them are progressively developed in the protagonist of the documentary.

Both overweight and obesity are associated with an increased risk of type 2 diabetes mellitus, hypertension, dyslipidemia, stroke, other cardiovascular derangements, fatty liver, musculoskeletal disorders, sleep apnea syndrome, other respiratory disorders and development of certain types of cancer. These associations translate into decreased life expectancy associated with excess adiposity and increased mortality rates.

In this link you can see an animated infographic from the Department of Endocrinology and Nutrition - Clinica Universidad de Navarra (Pamplona, Spain), which explains very clearly some aspects of obesity. In addition, you can download the illustrative chart, shown below:

Gene Therapy: Present and Future

Gene therapy is a technique using vectors, either viral or non viral, for introducing therapeutic genetic material into target cells to solve a specific problem.

The main events that led to the development of gene therapy include: 

• Discovery of DNA as the keeper of genetic information.
• Development of PCR.
• Sequentiation of the human genome.
• Finding of restriction enzymes.

In September 1999, 18-year-old Jesse Gelsinger took part in a gene-therapy clinical trial. The adverse patient reaction to an adenovirus vector during the clinical safety trial led to the realization that the failure to understand the biology of vector interactions with the human immune system could have fatal consequences. 

In April 2000, a paper published in Science marked the highest point in the history of gene therapy. It described the first gene therapy success in which three children were cured of a fatal immunodeficiency disorder, but this therapy has subsequently caused a leukaemia-like disease in 2 of the 11 patients who have been treated.

The efficiency of gene therapy mainly resides in vectors. Intense efforts have been pointed to understand the molecular basis of how viruses and viral vectors interact with the host. In this sense, an ideal vector should have the following features:

• Do not trigger immune response.
• Easy to prepare.   
• Enough capacity to harbour large genes.
• Act both in proliferating and in resting cells.
• Easily dirigible to the target cell.
• Survival during large periods of time in the infected/transfected cells.
• Have regulatory elements to correct gene expression.

Vectors are classified in viral and non-viral:

1. Viral vectors: Viral vectors were the first to be used, given its high efficacy as vehicles for nucleic acids. Viruses are composed of DNA or RNA surrounded by a protein capsid, and in some cases, a lipoprotein envelope. There are five main classes of clinically applicable viral vectors: retrovirus, lentivirus, herpes simplex virus-1, adenovirus and adeno-associated virus.

Taken from Thomas, Ehrhardt and Kay. Nat Rev Genet 2003.

 Steps in gene therapy using an adenovirus vector:

2. Non-viral vectors: This type of vectors represents an attempt to mimic the virus functions as transferring vehicles using synthetic systems, but reducing the adverse characteristics of viruses. Efficacy of infection is much lower as it has to overcome both external and internal barriers. Liposomes and naked DNA are the main useful types with the advantage of unlimited length of the genomic material that can be introduced. However, they are still less efficient than viral vectors.

A summary of the extra- and intracellular barriers faced by non-viral gene therapies following systematic delivery can be observed below:

Taken from Miyata et al. Chem Soc Rev 2012 and McCrudden and McCarthy. Cancer Gene Therapy – Key Biological Concepts in the Design of Multifunctional Non-Viral Delivery  Systems. Gene Therapy - Tools and Potential Applications. ISBN 978-953-51-1014-9.

Nowadays, the discovery of interference RNA has opened a new field concerning the control of gene expression.

Target cells are selected depending on the tissue in which the gene should be expressed. They must also be cells with a long half-life being important to consider the rate of division of the cells. Best target cells are hematopoietic stem cells but lymphocytes, respiratory epithelium, hepatocytes, fibroblasts and muscle cells are highly targeted in gene therapy.

In the following videos, the gene therapy procedures to Parkinson and tumoural diseases are explained:

1. Definition of gene therapy and main developments of the field.
2. Know the difference between in vivo and ex vivo.
3. Study the characteristics of an ideal vector.
4. Know the classification of vectors and types of genetic information inserted.
5. Familiarize yourself with the main applications used nowadays.

Practical Session 3 – Group 3

Remember that active participation in a reasonable and constructive way during the practical sessions as well as during the lectures scores positively for your final mark.

Lorenzo's Oil (1992)

Lorenzo’s oil is a drama based on real events. It tells the story of Lorenzo Odone who was diagnosed at the age of 5 years (in 1983) a rare and incurable disease, adrenoleukodystrophy (ALD), which causes a degenerative neurological condition leading to death in few years. There was no known treatment at that moment for ALD. The disease results in progressive deafness, blindness and paralysis. Soon after the diagnosis, his parents, with no medical or biochemical background, began a long struggle against illness seeking a treatment to save his son. The film was directed by George Miller, starring Nick Nolte and Susan Sarandon, and was nominated for two Academy Awards: Best Actress in a Leading Role (Susan Sarandon) and Best Writing, Screenplay Written Directly for the Screen (George Miller and Nick Enright).

ALD (also known as X-ALD, X-linked Adrenoleukodystrophy, Adrenomyeloneuropathy, Siemerling-Creutzfeldt Disease or Bronze Schilder Disease) is an X-linked hereditary disease affecting 1 in 20,000 males. It is caused by a deficiency of the protein ALD (ABCD1) whose function is to transport very long chain fatty acids (VLCFA) to the peroxisome for beta-oxidation. The lack of ABCD1 causes an accumulation of VLCFA in different tissues throughout the body, which produces an intense demyelination, leading to the development of severe neurological abnormalities and impaired vision, hearing and motor skills, leading to premature death.

The information about the disease is introduced gradually throughout the film, which contains many dramatic scenes; one of them being the moment in which Dr. Nikolais (Dr. Moser in real life) informs Lorenzo’s parents that the disease is hereditary and transmitted by the mother. The type of inheritance can be seen in the following schematic representation:

Super Size Me (2004)

Super Size Me is a documentary in which Morgan Spurlock investigates the effects of fast food in his own body, eating exclusively at McDonald's 3 times a day during one month. Throughout the experiment, he goes several times to different medical specialists to follow his evolution in terms of weight gain, changes in blood pressure and biochemical analyses. The results are surprising and interesting...

Obesity has become one of the leading causes of death and disability, threatening many of the health gains achieved during the last decades. Despite the alarm raised, the pandemic continues to grow without signs of abatement. The latest prevalence figures in the United States show that more than two thirds of Americans are overweight (68.5%) and 1 in 3 are obese (35.7%). Europe, in general, and Spain, in particular, follow the same trends observed in the USA. The prevalence of obesity in the Spanish adult population over 18 years, according to the results of the ENRICA study, is estimated to be 22.9% globally, being higher in males with 24.4% than in females with 21.4%. In the following video, several interesting numbers about the "weight of the world" are shown:

Imaging techniques

Since the times of Galileo, imaging has been considered the "eyes of science". Modern imaging technologies allow the visualization of multi-dimensional and multi-parameter data, leading to significant contributions to understanding biological processes. Different imaging techniques are described below:

  

   Endoscopy:

Endoscopy was first described by Hippocrates in Greece (460-375 BC). The first endoscope was developed in 1806 by Philipp Bozzini with his introduction of a "Lichtleiter" (light conductor). Endoscopy allows the inspection of the inside of the body using a (usually) flexible instrument called "endoscope".

Examples of endoscopy are bronchoscopy, colonoscopy, laparoscopy or gastroscopy, among others.

  

   X-Ray:

X-rays are a type of electromagnetic radiation which, since their discovery in 1895 by Roentgen, have been used in medicine for diagnosis and treatment, generating images of bones, organs, and internal tissues.

Current applications for this method are shown herein:

      1.- Conventional X-Ray. Radiographs are useful for the detection of pathology of the skeleton as well as for detecting some disease processes in soft tissues.

     2.- Computed tomography (CT). In CT, a low energy X-ray source and a detector around the subject is required, acquiring volumetric data. The cross-sectional images are used for a variety of diagnostic and therapeutic purposes:

     3.- Angiography.This imaging technique allows to visualise the trajectory and inside or lumen of blood vessels and organs.

CEREBRAL ANGIOGRAPHY

    Echography

It involves the use of high-frequency sound waves to create images of organs and systems within the body. Ultrasound has developed from 2D to 3D ultrasound recently giving enhanced diagnostic capabilities useful in obstetrics, gynecology as well as cardiology.

                                                        3D ULTRASOUND PICTURE

   Magnetic Resonance Imaging (MRI)

MRI is used in radiology to visualise internal structures of the body in detail by placing a subject in a strong magnetic field. In the clinical practice, MRI is useful for distinguishing altered from normal tissue. A MRI scan can reveal the gross anatomical structure of the human brain:

  Positron Emission Tomography (PET)

In PET, radioactive tracers are incorporated into metabolically active molecules and injected intravenously. PET is useful in system biology studies related to metabolism and metastasis. This method is especially used to detect tumor cells at an early stage as well as to diagnose neurodegenerative disorders such as Alzheimer and Parkinson disease as well as dementia.

 Artificially colour coded whole -body PET scan using 18F-Fluorodeoxyglucose (FDG) 

Imaging technology is in constant evolution, so numerous advances and improvements such as optical coherence tomography, electric impedande tomography, termography or hybrid PET-MR among others have been developed.

Which imaging technique has been used below? Can you identify the elements depicted?

The imaging technique used is MRI, that can reveal incredible data about a person's body, but also about differents elements such as fruits or vegetables, i.e. watermelon, pommegranate or cucumber!! Imaging techniques are not only used  for diagnosis but also for research purposes.

1.- Be able to identify different imaging techniques. 
2.- Know the main characteristics of imaging techniques used in medicine.
3.- Study the applications of the different imaging techniques.
 

New Technologies in Neurosciences

Neuroscience encompasses the study of the nervous system. It not only involves the study of its anatomy and physiology, but also the diagnosis and treatment of the pathologies in relation with the nervous system.

Thanks to past and present research, neuroscience has evolved from studying the anatomy and physiology of the brain to finding cures for complex neurological disorders. The genetic variation and non-Mendelian inheritance create a challenge in understanding neurological disorders that disrupt the normal processes of the brain such as Alzheimer’s disease. The following video shows the evolution of Alzheimer’s disease:

Due to advances in neuroscience the horizon looks brighter. Molecular biology has played an important role in understanding the genetic characteristics behind neurological disorders, but also imaging technologies are now contributing to a better understanding of the human brain. The Human Brain Project and the Brain Activity Map Project seek to integrate everything we know about the brain into massive databases and detailed computer models.

In this sense, in order to find a cure, researchers use different techniques in a multidisciplinary approach that spans from radiology to molecular biology. The Human Connectome Project aims to provide an unparalleled compilation of neural data as well as an interface to navigate across these data to achieve conclusions about the living human brain.

By understanding how the human brain works, we can effectively identify and target the affected areas that cause neurological diseases:

• The brain is an enormously complicated system of interconnected cells. Johnson and Wu suggest that the human brain has 10¹² neurons with 10¹⁵ synapses. The magnitude of 10¹⁵ synapses is about 222 times greater than the distance from Earth to Pluto in meters.  

• Sleep has an important role in memory. Recent studies have shown that presentation of smells or sounds that accompanied learning can enhance procedural and episodic memories when re-presented in sleep. Welberg L. Nat Rev Neurosci 2013, 14: 737. 

• In the 18th of October issue of Science a mechanistic explanation for how sleep, in addition to its well-described effects on memory consolidation, facilitates the clearance of potentially neurotoxic waste products that accumulate during wakefulness was published. Xie L. Science 2013, 342:373.

• Chronic pain is estimated to affect over one-quarter of the world's population, and presents a considerable therapeutic challenge. The aim is to understand the risk factors and mechanisms that underlie chronic pain to develop effective and non-addictive treatments for this condition.

• The Nobel Prize in Physiology or Medicine 2014 was awarded with one half to John O'Keefe and the other half jointly to May-Britt Moser and Edvard I. Moser "for their discoveries of cells that constitute a positioning system in the brain"

• Be able to identify different techniques applied to neuroscience research.
• Know the main imaging and molecular techniques used in neurosciences.
• Study new markers and treatments for neurological diseases.
• Know about surgical procedures in neuroscience.
• Concept of optogenetic technique. 

Pharmaceutical R+D

What is a drug?

In Pharmacology, a drug is a natural or synthetic substance able to produce biological or functional effect in a living organism. A medication is a drug used for the treatment, cure, prevention, or diagnosis of a disease as well as in some condition to enhance physical or mental well-being.

Preclinical phase

After the drug discovery, its biological activity is analysed in computational models, cell cultures or animals (from less to more sensitive according to their phylogenetic scale) following the 3 R's principle of Russell and Burch. The protocols must be submitted and approved by the Ethical Committee of Experimental Animal Research of the university or research centre where the research is going to be carried out. 

Preclinical studies are also required to determine the efficacy of the medicament via the pharmacokinetic (the response of the organism to the drug) and pharmacodynamic (how the drug acts in the organism) analyses. In addition, the security of the drug needs to be evaluated by toxicological studies after chronic and acute exposure.  An improper testing of the efficacy or security of the drugs can cause serious health problems in the clinical stage, as happened in the middle of the XX century with Thalidomide, a drug prescribed as a sedative and antiemetic for morning sickness. Thousands of pregnant women took Thalidomide to relieve their symptoms. In the late 50's and early 60's reports of children born with deformities such as phocomelia (rare congenital disorder involving malformations of the limbs, see picture in the right) as a consequence of Thalidomide use saw the light. The effects of Thalidomide raised the issue of safety of pharmaceutical drugs with testing and approval of toxins becaming more important.

After preclinical testing, the drug can progress to the clinical phase following the positive evaluation of the National (AEMPS: Agencia Española de Medicamentos y Productos Sanitarios in Spain), European (EMA: European Medicines Agency) or American (FDA: Food and Drug Administration) authorities.

Clinical phase 

The clinical phase includes a serial of tests to ensure the efficacy and security in humans as well as to generate data of the adverse drug reactions or adverse effects with other treatments. All the investigations must conform to the Declaration of Helsinki and the protocols must be submitted and approved by the Ethical Committee of Clinical Research. The clinical developmental phases are:

• Phase I: the drug is administered, for the first time, to 20-100 healthy individuals in order to evaluate the safety of the dosage and how the drug should be given. Usually this stage lasts from 6 to 12 months.
• Phase II:  the biological activity and the optimal dosage of the drug is tested in 100-200 patients and healthy individuals involved in blind clinical trials. Information about the drug's safety, side effects and potential risks are also collected. This phase of the clinical trial lasts between 1-2 years.
• Phase III trials enroll a large number of individuals (1,000-3,000 patients) in order to compare the efficacy of the new drug with other existing medicaments in a double-blind, randomized study. Additional information about the safety and side effects of the drug is gathered during a period of 2-3 years. Once the drug has been proven succesful in the Phase III clinical trial, the researchers can submit an application to AEMPS, EMA or FDA approval. If data from the clinical trial meet the AEMPS's, EMA's or FDA's standards of safety and efficacy, the drug is approved for a specific use.
• Phase IV or post-marketing surveillance: the safety surveillance is designed to detect any rare or long-term adverse effects over a large population. Harmful effects can result in a drug being withdrawn or restricted to certain uses. A recent example include rofecobix (Vioxx), a nonsteroidal antiinflammatory drug used for the treatment of osteoarthritis, acute pain and dysmenorrhoea, that was withdrawn from the market because it caused serious secondary cardiovascular effects.

The entire process of a drug from the lab to this point may take approximately 12-18 years. In the following video, you can see a summary of the 4 stages of the clinical phase:

You will have to know all the phases of the pharmaceutical R&D process as well as their main characteristics:

 

Scientific Writing

Today we have addressed the topic of how to present data in written form, focusing mainly on writing papers for biomedical journals. Why is writing important in science? Scientists need to communicate their findings and this is usually achieved via publishing their work in scientific journals. Thus, a critical aspect of the scientific process is to share your information and experience with the scientific community. Reporting your new results in biomedical journals is a quick way to disseminate the information to the specialized community contributing to increase the knowledge within a discipline as well as to help others interpret their own results.

Types of articles

We have mentioned in class the different types of articles and their main characteristics. While most articles published are original research papers, there are also reviews, editorials, commentaries, perspectives, case reports or letters to the editor, among others.



Fundamental style considerations

In the International Committee of Medical Journal Editors - ICMJE) you can find the Uniform Requirements for Manuscripts. Most biomedical journals have their own format, structure and writing styles. Therefore, it is important that you are familiar with the Instructions for Authors of the specific journal you aim to submit your manuscript.

Your text should conform to the conventions of standard written English (sentence form, grammar, spelling, etc.). Structure your sentences carefully using the basic division into subject, verb, and complement. In addition, the structure of the sentence will convey emphasis, draw attention to the most important part at the same time as help readers to interpret your meaning correctly. Moreover, you should structure your sentences and paragraphs to flow, conferring your article cohesion and coherence.
 
Your ideas will have little impact, no matter how good the research is, if they are not communicated effectively!

Keep in mind that scientific terminology has precise meaning. Thus, be certain you select your words correctly and adequately; write clearly and concisely. Writing and thinking are very closely linked, "fuzzy writing reflects fuzzy thinking". When people have difficulties in translating their ideas into words, it generally reflects that they may not be fully aware of what they want to transmit.

• Adapt to the special requirements of your selected audience, journal and type of article.

• Be precise and accurate: Scientific terminology carries specific meaning; learn to use it appropriately and consistently. In fact, it takes a deeper understanding to explain a complex topic simply and succinctly. 

• Be clear and concise: Write briefly and to the point. Say what you mean simply and clearly avoiding embellishment with unnecessary words or phrases. Brevity is very important. Do not use colloquial speech or slang; do not use contractions like for example "don't" or "isn't".

"Brevity is the soul of wit" (W. Shakespeare)

Considerations for the preparation of a research article

One of the initial considerations is to choose the appropriate readership for your article. Usually you will be writing to your peers. Knowing your audience will help you to decide what information to include. Obviously, you write a very different article for a highly specialized, technical, disciplinary journal as opposed to a more general publication that covers a broad range of disciplines.  Another relevant aspect to take into account is the impact factor of the journal. 

The first step in the process of writing is to order and organize the information you wish to present. Another critical point when preparing your first draft is to decide the authors and their specific order. The choice of a good title is also extraordinarily important; it should be informative at the same time as attractive and objective. Some people work well from an outline, others do not. Whatever system you follow, be aware that scientific writing requires special attention to order and organization. Because the paper will be divided into sections, you need to know what information will go into each.

The following video very nicely summarizes the main sections of an article and their content.

• You need to know the different types of articles (original research papers, reviews, editorials, commentaries, perspectives, case reports and letters to the editor, among others) together with their main characteristics and usefulness.

• In addition, you have to be familiarized with the main sections of a research article, how to structure and develop them in order to communicate effectively.