CBIO9: Cancer resistance, biomarkers and personalised treatment Flashcards

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1
Q

What is synthetic lethality?

A

Two hit mutation, where the first hit mutates again to cancel the effect of the second hit

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2
Q

Give an example of synthetic lethality

A
  • Both BRCA1/BRCA2 altered and PARP inhibited

- Secondary mutation in BRCA1/BRCA2 leading to resistance to PARP inhibition

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3
Q

When does cancer therapeutic resistance occur?

A

when cancers develop resistance to treatments such as chemotherapy, radiotherapy and targeted therapies, through various mechanisms

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4
Q

How can cancer therapeutic resistance occur?

A

pecific genetic and epigenetic changes in the cancer cell(s) and/or the microenvironment in which the cancer cells reside

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5
Q

What does tumour microenvironment include?

A

The tumour microenvironment includes non-cancerous cells within and adjacent to the tumour, and the proteins expressed by them that contribute to tumour growth.

For example, increased matrix stiffness of hepatocellular carcinoma cells promotes resistance to chemotherapy.

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6
Q

How can you overcome therapeutic resistance in cancer? (4)

A

1) Using an alternative drug that works via different mechanisms.
2) Understanding exactly how drug resistance develops in cancer. This allows for the possibility of designing drugs to specifically target it.
3) Applying a combination of therapies to target different aspects of the tumour. This reduces the opportunities for the tumour to become resistant.
4) By personalising treatment. Choosing a treatment that is tailored to a specific patient significantly reduces rates of therapeutic resistance.

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7
Q

How many cases of chemotherapy failure are related to drug resistance?

A

90%

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8
Q

What are the two types of drug resistance?

A

Intrinsic

Acquired

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9
Q

What does intrinsic resistance relate to?

A

Drug resistance mechanism exists prior to treatment: tumours insensitive to chemotherapy are intrinsically resistant

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10
Q

What does acquired resistance related to?

A

Induced (selected for) by drug treatment: tumours that are mostly sensitive to chemotherapy will be significantly reduced, leaving few cells which may lead to acquired resistance

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11
Q

How is cell death induced following drug treatment (flow scheme basic)

A
  • absorption
  • distribution
    –> drug influx
    (drug activation [- drug inactivation/alterations in drug target) ->
    (cellular damage [-adaptive responses/dysfunctional apoptosis)
  • -> drug efflux
  • metabolism
  • elimination
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12
Q

How can the anticancer activity of a drug can be limited?

A
  • Poor drug influx or excessive efflux
  • drug inactivation or lack of activation
  • alterations such as changes in expression levels of the drug target
  • activation of adaptive pro-survival responses
  • lack of cell death induction due to dysfunctional apoptosis, which is a hallmark of cancer
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13
Q

Give 3 examples of how drug resistance can arise from decreased uptake of drug

A

1) Methotrexate (toxic folate analogue) resistance commonly occurs by mutation of one or both of the folate transporters. Folate is a vitamin that enters cells using the folate transporters found on cellular membranes. The anti-cancer drug methotrexate is a toxic folate analogue and also uses the folate transporters to enter cancer cells.
2) Resistance to nucleoside analogues (anti-cancer drugs that are similar to nucleotides) has been described as a result of mutation of specific nucleoside transporters.
3) Reduction in plasma membrane receptors and transporters and reduced endocytosis have been shown to occur in cisplatin-resistant cell lines that are resistant to the chemotherapy drug cisplatin.

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14
Q

Explain and give an example of drug resistance due to increased drug efflux

A

P-glycoprotein (Pgp), also known as MDR1 (multi-drug resistance protein 1), is an ATP binding protein pump in the cell membrane that pumps many foreign substances out of cells. Its over-expression is associated with drug resistance to Pgp substrates e.g. the chemotherapeutic drugs Doxorubicin, taxanes and vinca alkaloids.

Inhibition of Pgp with verapamil, for example, can reverse drug resistance in vitro. The clinical significance of MDR1 over-expression is disputed. There is good evidence to suggest that over-expression of this protein plays a significant role in drug resistance in cases of acute myeloid leukaemia and myeloma, but its role in drug resistance where solid tumours are concerned remains unclear.

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15
Q

Drug resistance can be due to altered drug metabolism to increase detoxification, which means the cancer drugs are no longer toxic. Give 3 examples.

A

Glutathione (GSH) is a powerful anti-oxidant that protects the cells against the damaging effects of reactive oxygen species. GSH conjugates to platinum chemotherapy drugs (e.g. oxaliplatin and cisplatin) and modifies them to substrates for ABC transporters, which facilitate drug efflux.

CYP450, an enzyme found in the liver, can inactivate irinotecan (Topoisomerase I inhibitor, used in colon cancer).

Metallothionein (MT), a protein found on the membrane of Golgi apparatus, also binds platinum drugs and inactivates them.

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16
Q

Drug resistance can be due to altered drug metabolism to decrease activation, which means cancer drugs are not activated within cancer cells. Give an example.

A

Cytarabine (also known as AraC), a nucleoside analogue widely used for the treatment of acute myeloid leukaemia (AML), requires phosphorylation to be activated by the enzyme deoxycytidine kinase. Resistance to cytarabine develops when levels of deoxycytidine kinase are reduced, through downregulation or mutation.

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17
Q

alterations of th drug target, such as mutations or altered expression levels, can promote development of drug resistance. Give an example.

A

Gleevec is an anti-cancer drug that targets the BCR/ABL protein in chronic myeloid leukaemia. Drug resistance develops as a result of mutations occurring at the binding site of the drug within the BCR/ABL protein.

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18
Q

Drug resistance can be due to changes in cellular pathways such as DNA repair pathways. Give an example.

A

Resistance to the DNA damage-inducing drug cisplatin occurs due to enhancement in DNA repair mechanisms. This can be due to high expression of important components such as ERCC1, an important factor in the NER (nucleotide excision repair) DNA repair pathway.

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19
Q

Drug resistance can be due to changes that result in evasion of apoptotic pathways. Give two examples.

A

Inactivating mutations in genes coding for apoptotic proteins, such as p53.

Activating mutations in genes coding for anti-apoptotic proteins, such as Bcl-2.

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20
Q

When does collateral sensitivity occur?

A

resistance to the first one given drug confers a hypersensitivity to an alternate cytotoxic agent to which parental cells were not originally sensitive. The same genetic alteration that caused resistance to one drug now sensitises them to another.

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21
Q

Give an example of collateral sensitivity arising

A

A patient with metastatic anaplastic lymphoma kinase (ALK)-rearranged lung cancer was resistant to crizotinib because of a mutation in the ALK kinase domain. The patient responded to another drug, lorlatinib. When the tumour relapsed, sequencing of the tumour revealed an ALK mutation resistant to lorlatinib in addition to the mutation resistant to crizotinib. However, the new mutation enhanced binding to crizotinib, negating the effect of first mutation and re-sensitising resistant cancer to crizotinib. The patient received crizotinib again, and cancer-related symptoms resolved.

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22
Q

What are cancer stem cells?

A

cancer stem cells (CSCs, or cancer cells with stem-cell-like properties) are (or are postulated to be) rare immortal cells within a tumour that can both self-renew by dividing and also give rise to many cell types that constitute the tumour and can therefore form tumours. Only a small subset of cells can give rise to a new tumour.

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23
Q

What characteristics are believed to make CSCs highly resistant to conventional chemotherapies?

A
  • high expression of ATP-binding cassette (ABC) transporter proteins
  • high aldehyde dehydrogenase (ALDH) activity, which oxidises and detoxifies several substrates
  • expression of anti-apoptotic proteins such as Bcl-2 and Bcl-XL
  • enhanced DNA damage repair
  • activation of key pro-survival signalling molecules such as NOTCH and nuclear factor-κB
  • relatively quiescent – chemotherapy targets rapidly dividing cells
24
Q

What are the three models for the mechanisms of drug resistance?

A

Following chemotherapy:

1) cancer cells resistance to chemotherapy due to a somatic mutation still present
2) Stem cells that are drug insensitive to chemotherapy due to relative quiescence, in the absence of resistant somatic mutated cells, these will not cause a relapse
3) these can cause two relapses leading to chemo resistance

25
Q

Describe the models of resistance in more detail

A

1) Somatic mutation model – resistant cells continue to grow to cause relapse and cannot be targeted by further chemo
2) Cancer stem cells – remain unaffected by chemo and persist after chemo and cause relapse when cells exit G0
3) Combined – in practice both processes occur concurrently and relative proportions vary between patients

26
Q

Define epigenetics

A

Changes in gene expression (activating or inactivating) that are not due to the DNA sequence. These can be somatically inherited through cell division.

27
Q

What does the high level of epigenetics lead to in cancer cells?

A

It creates diversity in gene expression and during drug treatment, which could lead to the development of acquired drug resistance.

28
Q

Describe drug resistance can be acquired by epigenetics in cancer cells

A

When a tumour containing cells with diverse gene expression (known as heterogeneity) is treated with a drug, most cells will die but some may become resistant due to leaving some cells that have undergone epigenetic changes and will survive. This leads to tolerance of treatment

29
Q

What are cells that have developed resistance to chemotherapy through epigenetic modifications called?

A

Epigenetically poised persistent tumour sustaining cells

30
Q

Why are treatment resistance cancer cells given the name ‘epigenetically poised persistent tumour sustaining cells’

A

because chromatin domains have both the activation-associated histone modification and the repression-associated modification

31
Q

If the chromatin modification that confers tolerance to drug is lost, then tolerance can be reversed, what are the two possible outcomes for these cells?

A

1) Chemo-sensitive relapse – tolerance reversal rendering tumour cells sensitive to chemotherapy again
2) Chemo-resistant relapse – further exposure to chemotherapy ‘locks-in’ epigenetic states and fixates gene expression to select for drug-resistant tumour cells.

32
Q

T or F:
Many anticancer drugs require metabolic activation and thus cancer cells can develop resistance through decreased drug activation.

A

True

33
Q

What is the difference between intrinsic and acquired drug resistance?

A

Intrinsic means the drug resistance mechanism exists prior to treatment, acquired means drug resistance is induced by drug treatment.

34
Q

What is the meaning of ‘altered drug targets’ in drug resistance?

A

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

35
Q

What are cancer stem cells?

A

Rare immortal cell within a tumour that can both self-renew by dividing and give rise to many cell types that constitute the tumour, an can therefore form tumour

36
Q

What are substances produced by cancer cells, or by other cells of the body in response to cancer called?

A

Cancer biomarkers

37
Q

How are cancer biomarkers distinguishable from other body cells?

A

Tumour biomarkers may be produced at higher or lower levels under cancerous conditions

38
Q

What can cancer biomarkers determined in?

A

1) Circulation - whole blood, serum, plasma
2) Stool or urine
3) Ejaculation
4) Sputum
5) Nipple discharge
6) Biopsy or special imaging

39
Q

Give examples of what biomarkers can include and how?

A

DNA, RNA, proteins, peptides and biomolecule chemical modifications associated with cancer due to germline and somatic mutations, transcriptional changes, and post-translational metabolism.

40
Q

What are biomarkers able to do?

A

Biomarkers can differentiate affected and unaffected patients and well as distinguish patients in different stages of disease.

41
Q

What is the clinical limitation of cancer biomarkers

A

No universal tumour marker and noncancerous conditions cause increased biomarker levels – a clinical limitation to their use

42
Q

The identification of biomarkers has several applications, what are they?

A

1) Estimating risk of developing cancer
2) Screening for signs of primary cancer
3) Diagnosis
4) Prognosis
5) Predicting efficacy of therapy for given patient
6) Monitoring

43
Q

How can you estimate the risk of developing cancer?

A

It can can be done through genetic testing for the loss-of-function BRCA1 mutation which is implicated in breast and ovarian cancer. This allows individuals to opt for more intensive screening, chemoprevention with tamoxifen or prophylactic surgery.

44
Q

What type of screening can take place and why is it necessary?

A

In otherwise healthy patients, especially older, to check for malignancy. The gFOB (guaiac Faecal Occult Blood) test screens for bowel cancer in those over 55.
Diagnosis of cancer using histologic evaluation of biopsies can determine whether lung nodules are cancerous. Identifying the BCR-ABL fusion gene in the blood or bone marrow can confirm a chronic myeloid leukaemia diagnosis.

45
Q

What can prognosis be determined by?

Give an example

A

by biomarkers to examine gene expression signatures. This is especially true in breast cancer where the tumour is assessed using the 21-gene recurrence score.

46
Q

Describe the application of predicting treatment efficacy

A

It can also be done using genetic analysis as colorectal cancer patients with KRAS mutations show a poor response to anti-EGFR therapies.

47
Q

Describe the purpose of monitoring biomarkers

A

such as carcinoembryonic antigen (CEA) in colorectal cancer, can help keep track of how well cancer treatments are working and assess whether the patient has relapsed.

48
Q

List the strategies for discovering biomarkers?

A
  • Gene expression profiling
  • MS based profiling
  • Peptidomics
  • Biomarker family
  • Secreted factors
  • Protein arrays
  • Autoantibodies
  • MS imaging of tissue
  • Gene fusion/translocations
  • Serum proteomics
49
Q

Describe the strategies for discovering biomarkers?

A
  • Gene expression profiling – measurement of activity in thousands of genes at once in order to create a global picture of cellular function
  • MS based profiling – mass spectrometry to prolife metabolites in a tissue
  • Peptidomics – direct measurements of endogenous peptides in a biological sample through MS
  • Biomarker family – examining whether other members in the family of an existing biomarker may be cancer biomarkers
  • Secreted factors – proteins or nucleic acids secreted by cancer cells found in surrounding environment or blood
  • Protein arrays – monitor protein levels and activity on a large scale
  • Autoantibodies – TAAs elicit and immune response and autoantibodies would be produced
  • MS imaging of tissue – technique used to visualise the spatial distribution of molecules by their molecular masses.
  • Gene fusion/translocations – looking for gene fusion due to translocation
  • Serum proteomics – MS used to identify protein composition of serum.
50
Q

What are the 5 stages of biomarker discovery and development?

A

1) Preclinical exploratory studies – differences between non-tumour and tumour specimens compared
2) Assay development and validation – assay to discriminate affected and unaffected patients must be developed
3) Retrospective longitudinal clinical repository studies – specimens collected from healthy cohort monitored for cancer development used to asses capacity of the biomarker to detect preclinical disease.
4) Prospective screening studies – individuals screened with the assay and established diagnostic procedures used on patients that screened positive to establish tumour stage at time of detection.
5) Randomised control trials – non-biased study in which people are randomly assigned to groups to determine if screening reduces cancer burden on population.

51
Q

What does the iKnife do?

A

It cuts the tissue and gaseous molecules are collected and identified by MS to determine whether the tissue is normal or malignant. This avoids the problem of residual tumour tissue left behind after surgery. The biomarkers used are phospholipids from cell membranes as the phospholipid biosynthesis pathways are different between healthy and malignant tissue, due to uncontrolled proliferation.

52
Q

T or F:

A given biomarker can be used in more than one way, such as for cancer diagnosis as well as recurrence.

A

True

53
Q

What is a biomarker used by iKnife?

A

Phospholipids

54
Q

What is personalised treatment? (stratified medicine)

A

It classifies tumours based on their genetic makeup, rather than their location, to strategise a treatment plan

55
Q

What are the three considerations when performing personalised treatment? Describe them

A

1) Identifying who to treat – understanding mechanism by which a treatment kills tumour cells and developing biomarkers to identify the patients who will benefit from the treatment
2) Combating drug resistance – understanding mechanism of resistance and developing biomarkers to predict when this will occur and delaying resistance
3) Optimising combination therapy – understanding why drug combinations work and how they can be used to combat resistance. Predictive markers developed to assess whether combinations are effective in patients.

56
Q

Explain the procedure for adoptive T-cell therapy into a patient (case study)

A

1) Whole-exome sequencing (WES) and RNA sequencing (RNA-seq) of tumour revealed 62 somatic mutations
2) Initially screened against all of the mutations by using pulsed peptide pools or transfected mRNAs (tandem minigenes (TMGs) expressed in autologous antigen-presenting cells (APCs)
3) TIL populations derived from culturing small pieces of the patients tumour in high-does IL-2
4) Reactive against mutant versions of four proteins - SLC3A2, KIAA0368, CADPS2 and CTSB
5) Lymphodepletion and addition of checkpoint blocker before reinfusion of TIL
6) 6-weeks after cell transfer, the target tumour burden had reduced by 51%.. over time this amounted to 0 tumour left