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Exam 2008-01-11

Molecular Oncology and Biostatistics Biomedicine program, T5

Name:________________________

Code:__________________________

Good luck!

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Exam 2008-01-11

Molecular Oncology and Biostatistics Biomedicine program, T5

Writing hours: 10.00-14.00

Code:________________________ Max: 90p Pass: 54p Pass with distinction: 72p

Good luck!

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1. Explain the following tumor biological terms: (4p)

a) Proto-oncogene gene

b) Immortalisation

c) Cancer stem cell

d) The restriction point 2. Explain the following clinical oncology terms: (4p)

a) Brachytherapy

b) Cytology

c) Neo-adjuvant treatment

d) Palliative treatment

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3. Immunotherapy is an evolving field in the treatment of cancer

patients.

a) Please give three examples of strategies for immunotherapy

against cancer. (3p)

b) Please discuss and reflect upon the difference between the way in

which the immune system recognizes infected versus cancer cells.

(2p)

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4. Tyrosine kinases are common targets for novel anticancer drugs. a) In this respect, please fill in the missing words marked with X in the table. (3p) drug target protein target cell one approved indication x x x adjuvant treatemnt of breast cancer x VEGF x x Glivec/imatinib x x x b. Please describe the dominating activating mechanism for the

following tyrosine kinases; c-kit in GIST tumors, bcr-abl in CML and

HER2/ErbB2 in breast cancer. (3p)

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c. Please describe the putative molecular features of an initially

HER2 positive breast cancer that no longer responds to trastuzumab,

but shows a good response to lapatinib/Tykerb™ treatment. (2p)

5. It is increasingly recognized that post-translational regulation is important in tumor development. One such process is the ubiquitin proteosomal system (UPS). a) Give an example of how you can show that a protein is degraded by the UPS. (1p)

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b) Also, give examples of a known oncogenic protein as well as tumor

suppressor protein that is dysregulated in cancer cells due to faulty

UPS degradation. (2p)

6.

a) Please mention three reasons for the fact that the breast cancer

incidence in developing countries is approximately only one third of

that in industrialized western countries. (3p)

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b) In Sweden fortunately > 90% of all breast cancer patients survive

more than five years. This was far from the case 30 years ago. Please

mention the most probable reasons for this dramatic improvement of

prognosis. (2p)

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7. The finding of oncogenes and tumor suppressor genes has opened

up for the development of new drugs and diagnostic procedures. In

some diseases such as breast cancer we still probably only know a

fraction of the genes involved.

a) Please suggest and explain a strategy for finding new oncogenes

and tumor suppressor genes involved in breast cancer

development. Please also discuss the pros and cons of the

proposed strategy. (3p)

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b) You were very successful in your strategy and found a new

putative important cancer gene in breast cancer. Suggest key features

/ experiments that would strengthen the notion that the candidate

gene found is indeed an oncogene or tumor suppressor gene involved

in breast cancer development. (4p)

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8. The p53 gene is a key tumor suppressor gene mutated in > 50% of

all human tumors. The p53 pathway can also be altered in tumor

cells by other means than changes of the p53 gene itself.

a) Please mention three such other alterations, and explain why these

alterations also lead to an impaired p53 function. (3p)

b) Tumor formation includes changes in at least six types of cellular

programmes. Please describe how the p53 molecule is normally

activated upon stress, and how this leads to changes in two of the six

cellular programmes alluded to above. (3p)

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9.

a) Name one genetic aberration associated with the age-peak (2-5

years at diagnosis) in childhood leukemia and one aberration,

sometimes present in the leukemic clone of children, not associated

with this age-peak. (1p)

b) A colleague comes to you with a newly issued paper describing a

new genetic aberration in childhood ALL. The paper is based on

preserved leukemic specimens from the 1980s in Greece analysed for

a gene encoding a signal-transduction protein involved in

proliferation and apoptosis. The results clearly suggest that

inactivation of the gene is associated with poor outcome and your

colleague suggests that you should incorporate a test for mutation of

this gene into your treatment-stratification. You hesitate.

Give your best reason, why more information is needed before the

results from the English study can be applied in the stratification of

Swedish patients. (2p)

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10. Researchers want to study the effects of a combination of

zoledronic acid (ZOL) and docetaxel (Doc) on a prostate cancer

xenograft. For this purpose, they have injected the right tibiae of

twenty male SCID mice with prostate cancer cells. The animals

were randomized into four equal groups when tumors were

established: 1) a control group which received saline injections, 2)

a ZOL treatment group which received injections of ZOL twice a

week, 3) a Doc treatment group which received injections of

docetaxel every two weeks, and 4) a group treated with a

combination of ZOL + Doc which received ZOL twice a week and

docetaxel every two weeks. As outcome, the researchers have

recorded the tumor volume as percentage of the total volume

(%TuV/TV) in the longitudinal section of the tibiae. The resulting

means and standard errors are shown in the graph below.

Source: PMID 16417633

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a) Describe this design. (1p) b) Interpret the following ANOVA table at a significance level

of 5%: Df Sum Sq Mean Sq F value Pr(>F) Doc 1 80.0 80.0 1.55 0.2308 ZOL 1 1125.0 1125.0 21.82 0.0003 Doc:ZOL 1 20.0 20.0 0.39 0.5422 Error 16 825.0 51.6 Which treatments have significant effects? Is there a synergy effect between docetaxel and ZOL? (2p)

c) Does the plot of the data above agree with the results of the ANOVA? Explain briefly. (1p)

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11. A research group wants to use retinoblastoma cell lines for screening candidate drugs. In a typical experimental setup, two groups of cell lines will be run in parallel, one treated with the potential new drug, the other as control group. The outcome of interest is the proliferation rate of the cell lines. Based on previous experiences, the researchers estimate that the proliferation rate for an untreated cell line will be 0.80, with a standard deviation of 0.15. A candidate drug is considered for further study if it can reduce this proliferation rate by 15-20%.

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a) How many cell lines per group are required to have an 80% chance of detecting such a reduction in proliferation (testing at a significance level of α=0.05)? Motivate your answer, and show all calculations. (2p)

b) For budget reasons, the head of the research group decides to

run these experiments with only ten cell lines per group. Discuss briefly: How does this affect the chances of finding a promising drug? How can the experiment be changed to keep the power at 80%? (2p)

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12. A new drug is supposed to reduce common side effects of standard chemotherapy in breast cancer patients. A clinical trial has been proposed to study this claim, where the new drug will be compared with standard care. Three different hospitals will recruit patients for this study. Describe and discuss briefly a study design that takes into account possible systematic differences between hospitals. (2p)

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13. During Lab 5, we studied event-free survival of children aged 0-18 years diagnosed with acute lymphoblastic leukemia in the Nordic countries. We will now revisit these data to study whether event-free survival differs between patients with and without a particular chromosomal aberration. Recall that, when studying event-free survival, an event may be either relapse, death in remission, induction failure, resistant disease, or second malignant neoplasm. You may, however, refer to the outcome as ´the event’ or ´event’. Stata was used to fit a Cox proportional hazard model with the following explanatory variables: aberration patient has genetic aberration (=1) or does not (=0) sex sex of patient (0=male, 1=female) wbcclass categories for white blood cell count (1=lowest, 5=highest) ageclass age in 3 categories (1=infants, 2=1-9 years, 3=10 -18 years) . xi: stcox aberration sex i.wbcclass i.ageclass i.wbcclass _Iwbcclass_1-5 (naturally coded; _Iwbcclass_1 omitted) i.ageclass _Iageclass_1-3 (naturally coded; _Iageclass_1 omitted) failure _d: outcome analysis time _t: efsurvtime id: nophonr Cox regression -- Breslow method for ties No. of subjects = 2768 Number of obs = 2768 No. of failures = 597 Time at risk = 203302.4342 LR chi2(8) = 206.07 Log likelihood = -4429.2793 Prob > chi2 = 0.0000 ---------------------------------------------------------------------------- _t | Haz. Ratio Std. Err. z P>|z| [95% Conf. Interv] -------------+-------------------------------------------------------------- aberration | 1.739697 .3728996 2.58 0.010 1.1429 2.6480 sex | .8188432 .0695005 -2.35 0.019 .6933 .96704 _Iwbcclass_2 | 1.042807 .1084928 0.40 0.687 .85044 1.2787 _Iwbcclass_3 | 1.653188 .232428 3.58 0.000 1.2550 2.1777 _Iwbcclass_4 | 2.285549 .3329779 5.67 0.000 1.7178 3.0409 _Iwbcclass_5 | 4.34031 .5950664 10.71 0.000 3.3176 5.6784 _Iageclass_2 | .3619012 .0620159 -5.93 0.000 .25866 .50635 _Iageclass_3 | .513834 .0928143 -3.69 0.000 .36064 .73211 ----------------------------------------------------------------------------

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a) Do patients with the genetic aberration have higher or lower risk of suffering an event than patients with the same age, sex and white blood cell count, but without the aberration? Quantify your answer (i.e., how much more or less likely?), and argue whether the effect is significant. (2p)

b) The confidence interval for _Iageclass_3 has been omitted from the output. Would the CI most likely be (0.36-0.73), (0.42-1.13), or (1.13-1.67)? Motivate your answer. (2p)

c) How much bigger or smaller is the risk of suffering an event for a girl that has the aberration compared to a boy who does not have the aberration? Write down your calculations (two significant digits are enough). (2p)

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d) If we ignore all other parameters and compare events only between patients with and without the aberration (i.e. two groups), we find a hazard ratio of 2.03. How does this compare with the full model above? Explain your answer briefly. (2p)

e) Is this study best categorized as ecological, cohort, case-control, or cross-sectional? Motivate your answer. (1p)

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Essay questions: I. Imagine you are an epithelial cell in a human body. You are normally very well behaved and only proliferate when instructed to do so. a) Please describe the machinery that normally controls your ability to stay in a resting state and how this machinery is changed to eventually allow you to enter S-phase. (5p) b) You have the desire to start the path towards the more antisocial and egoistic behaviour of a tumor cell by acquiring mutations in genes that will make you proliferate in an uncontrolled manner. Please describe what genetic changes that you would likely primarily acquire, and the consequence of these mutations. (4p) c) Your host is not very happy with your uncontrolled behaviour and has decided to administer treatment that will specifically block your ability to proliferate in this manner. Please suggest two (existing or futuristic) approaches for such a therapy. (2p)

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II. A patient with suspected lymphoma requires good diagnostics.

a) Describe the principles for modern lymphoma diagnostics, and

motivate why the different components are needed. (5p)

b) Follicular lymphoma is one of the most common forms of

lymphoma. It generally has a specific genetic aberration. What is this

aberration, and how can it explain the typical clinical picture and

cure rate in follicular lymphoma? (3p)

c) The gene product of the genetic aberration mentioned above is

part of a family of proteins. Please describe in principle how the

different protein family members in this family interact to regulate

an important cellular process which is dysregulated in follicular

lymphoma cells. (3p)

d) Following your master’s degree in biomedicine you get a job at a

small new pharmaceutical company. You are asked to propose the

concept of two new drugs targeting the gene mentioned above. Please

describe two plausible existing or futuristic such concepts, and

comment on their pros and cons as new drugs for follicular

lymphoma. (4p)

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