CBIO 9: Cancer Resistance, Biomarkers and Personalised Treatment Flashcards

Question

What are the two possible outcomes for epigenetically poised persistent tumour sustaining cells?

Answer 1

1. If tolerance is reversed, tumour cells will become sensitive to the drug again (chemo-sensitive relapse). 2. However, exposure of poised cells to further chemotherapy and selection can ‘lock in’ an epigenetic state and fix gene expression. - This results in proliferation of a drug-resistant population of tumour cells (chemo-resistant relapse).

Answer 2

- Changes, such as mutations or modifications of expression levels, of the drug target that lead to cancer cell death

Answer 3

- Cells in which chromatin domains have both the activation-associated histone modification and the repression-associated modification

Answer 4

- Cancer biomarkers are substances produced by cancer cells, or by other cells of the body in response to cancer. - Most tumour markers are made by normal cells as well as by cancer cells; however, they are may be produced at much higher (or sometimes lower) levels under cancerous conditions.

Answer 5

- Some biomarkers can be detected in the circulation (whole blood, serum, or plasma), or in excretions or secretions (stool, urine, sputum, ejaculate, or nipple discharge). - In these cases, the presence of the biomarker can be assessed and/or or changes in its levels measured easily over time. - Due to the way the samples are taken collection is relatively non-invasive. - However, other biomarkers are within tissue, and require either a biopsy or special imaging so that they can be evaluated. - Cancer biomarkers are biomolecules such as DNA, RNA, proteins, peptides, and biomolecule chemical modifications. - The alterations associated with cancer can be due to a number of factors, including germline or somatic mutations, transcriptional and epigenetic changes, and post-translational modifications. - A collection (termed a signature), of transcriptomic (gene expression), proteomic, or metabolic changes can also serve as biomarkers. - Biomarkers typically differentiate between an affected patient from a person without the disease and/or they may also distinguish between different stages of disease. - Many different tumour markers have been characterised and are in clinical use. - Some are associated with only one type of cancer, whereas others are associated with two or more cancer types. - No “universal” tumour marker which can detect any type of cancer has been found.

Answer 6

- Sometimes, non-cancerous conditions can cause the levels of certain tumour biomarkers to increase, meaning the biomarker is not specific for cancer. - An example is prostate specific antigen (PSA) for prostate cancer, which you learnt about in CBIO6 where levels of PSA can be raised in benign prostatic hyperplasia. - Furthermore, not everyone with a particular type of cancer will have a higher level of a particular tumour marker associated with that cancer. - Moreover, tumour markers have not been identified for every type of cancer.

Answer 7

1. Estimating risk of developing cancer 2. Screening for signs of primary cancer 3. Diagnostic 4. Prognostic 5. Predicting whether a therapy will work for a given patient 6. Monitoring

Answer 8

- Biomarkers have been identified that can be used to determine an individual’s risk of developing cancer. - For example, a woman with a strong family history of ovarian cancer can undergo genetic testing to determine if she is a carrier of a predisposing germline mutation, such as loss-of-function mutation of BRCA1, which will increase her risk of developing breast and/or ovarian cancer (Easton et al, 1995, Am J Hum Genet 56: 265–271). - If so, she can opt for more intensive screening, chemoprevention with tamoxifen (a type of hormone therapy), or prophylactic (preventative) surgery. - Remember a germline mutation in BRCA1 increases risk but does not mean for sure the pa will develop the disease (why? think back to earlier modules).

Answer 9

- Biomarkers can be used to screen otherwise healthy patients for malignancy. - Screening programmes are often offered to older people who are more at risk of developing cancer. - An example is the use of the gFOB (guaiac Fecal Occult Blood) test in bowel cancer screening for those over 55 years old. - The gFOB test detects hidden blood (fecal occult blood) in faeces. - This could also be termed early diagnostic testing.

Answer 10

- A diagnostic biomarker is used to identify whether a patient has cancer. - For example, if a patient is found to have a lung nodule on their chest CT scan, histological evaluation of the biopsy specimen can determine whether the tissue is cancerous. - Another example is the discovery of the BCR-ABL fusion gene (Philadelphia chromosome) in blood or bone marrow, which is used to confirm a diagnosis of chronic myeloid leukaemia.

Answer 11

- “Prognosis” means the likely outcome of the disease. - In patients who have been diagnosed with a cancer, biomarkers can help determine prognosis (likely outcome), disease progression or likelihood of disease recurrence. - Traditionally, the clinicopathologic characteristics (signs and symptoms) of a tumour were used to determine the prognosis. - More recently, newer technologies are being utilised to assess prognosis for individual tumours. - For example, in breast cancer, there are a number of gene expression signatures developed that can be used to estimate prognosis for an individual patient based on analysing the tissue from tumour. - The best characterised of which is called the 21-gene recurrence score.

Answer 12

- Biomarkers can also be used to predict how well a patient will respond to a given treatment, or for determining which therapy is likely to be most effective. - In colorectal cancer, KRAS is a predictive biomarker, because somatic mutations in KRAS are associated with poor response to anti-epidermal growth factor receptor (EGFR) directed therapies.

Answer 13

- Biomarkers can be used to monitor status of the disease, either to detect recurrence or determine response or progression to therapy. - For example, Carcinoembryonic antigen (CEA) is monitored in colorectal cancer and some other cancers to keep track of how well cancer treatments are working or check if cancer has come back.

Answer 14

- Gene expression profiling - the measurement of the expression of thousands of genes at once which creates a global picture of cellular function. - This can be done by analysing tumour tissues from patient cohorts using RNA-sequencing. - MS-based profiling – using mass spectrometry (MS) to profile (often small) metabolites in a tissue (for an example see the iKnife later on). - Peptidomics - using mass spectrometry, this is the direct measurement of the endogenous peptides present in a given biological sample. - Biomarker family – this approach is sometimes employed if a member of a protein family is already an established biomarker and scientists will study other members of that family as they may also be good cancer biomarkers. - Secreted factors – proteins or nucleic acids which are secreted by cancer cells that can be found in the surrounding environment of tumour or in blood. - Protein arrays - this is a method used to monitor the levels and activities of proteins on a large scale. - Auto-antibodies – tumour-associated antigens could serve as biosensors for cancer because tumours naturally elicit an immune response in the host and produce auto-antibodies. - MS-imaging of tissue - this is a technique used to visualise the spatial distribution of molecules by their molecular masses. - Gene fusion/translocations – studying whether there have been gene fusion due to a chromosomal translocation (in all cancers not just haematological cancers). - Serum proteomics – using mass spectrometry to identify the protein composition of serum (also applicable to other biofluids).

Answer 15

1. Preclinical exploratory studies - In this phase, tumour and non-tumour specimens are compared to find differences between them. - If strong evidence is found this will generate hypotheses for clinical tests to detect cancer. - Strategies for cancer biomarker discovery discussed above can be used in this phase. 2. Assay development and validation - A clinical assay that uses a specimen of choice (preferably something that can be obtained non-invasively, or with minimal invasion) is developed in this phase. - The assay must discriminate individuals with cancer from those without. - The patients assessed in this phase have established disease. - The utility of the assay in detecting early disease is not demonstrated in this phase. 3. Retrospective longitudinal clinical repository studies - Specimens are collected and stored from a cohort of healthy (at the time) individuals who were monitored for development of cancer. - Using these specimens is its demonstrated that the biomarker has the capacity to detect preclinical disease and criteria for 'positive' screening results are defined. 4. Prospective screening studies - In this phase, individuals are screened with the assay together with the use of established diagnostic procedures to those who screened positive. - (This can help to establish the tumour stage or the nature of the disease at the time of detection). 5. Randomised control trials - A non-biased study in which a number of similar people are randomly assigned to a group where they are screened for the biomarker or assigned to a group where they are not screened. - The objective of this phase is to determine if screening reduces the burden of cancer in the population

Answer 16

The iKnife burns tissue as it cuts, and the gaseous molecules are collected and identified in real time by a mass spectrometer (see diagram and video below). The molecular pattern will distinguish whether the tissue is normal or malignant. If it is malignant the surgeon can remove it immediately, without the need for secondary surgery. This avoids the problem of residual tumour left behind after surgery. In the case of the iKnife, the biomarkers used to distinguish between normal and malignant tissue are phospholipids that compose cellular membranes. An important hallmark of cancer is uncontrolled cellular proliferation, requiring an increased rate of biological membrane synthesis that is orders-of-magnitude higher than healthy tissue. Consequently, phospholipid biosynthesis pathways differ between healthy and malignant tissues.

Answer 17

- personalised treatment, also known as stratified medicine, classifies tumours according to their genetic makeup instead of where they grow in the body - this information can be used to strategise a treatment plan for a particular patient

Answer 18

- Identifying who to treat: - this is achieved by identifying the exact mechanism of how a given treatment kills tumour cells and using this information to develop biomarkers to identify those patients in which the treatment will work - Combating drug resistance: - achieved by understanding the mechanisms behind treatment resistance and developing biomarkers to predict when this will occur - as well as using clinical approaches to prevent or delay resistance - Optimising combination therapy: - achieved by understanding why some drug combinations work, how combinations can be used to combat drug resitance and finding predictive markers to show if the combinations are working in patients

Answer 19

- In essence, tumour cells from this patient were DNA sequenced to identify mutations. - T-cells were isolated from the same patient’s blood and exposed to these tumour mutations via APC cells. - Following this, the T-cells were cultured with a small piece of the patient’s tumour to activate them. - The activated T-cells were selected, expanded and reinfused back into the patient. - The activated T-cells specific for the tumour mutation will seek, infiltrate and mount an immune attack against tumour cells in this patient.