Applied Medical Biotechnology

Vakinformatie

Given by Philippe Van den Steen, Diether Lambrechts and Jan Cools. Each professor gave 4 classes. Each part has the same weight on the exam and one part is oral with written preparation. At the end of each chapter of the classes of professor Lambrechts are possible exam questions (questions are guaranteed to be from that list). This is a subject from the faculty of bioscience engineering. (2024-2025)

ECTS-fiche: https://onderwijsaanbod.kuleuven.be/syllabi/e/I0I27AE.htm#activetab=doelstellingen_idp1519328

Exam questions

15 January 2026

Oral parts were with Cools or Van der Steen

Cools:

1. In a whole genome study on 100 patients they found the following mutations: What can you conclude from this? Wat advise would you give these patients? What risks do these patients have?
   • 3 patients with DNMT3A mutants: VAF=0.02, VAF = 0.01, VAF = 0.05
   • 1 patient with a TET2 mutant: VAF = 0.01
   • 1 patient with mutations in DNMT3A (VAF = 0.49), TET2 (VAF = 0.38) and P53 (VAF = 0.26)
2. 4 Concepts to explain
   • PROTAC
   • CAR-T cell therapy
   • Irreversible vs reversible kinase inhibitor
   • How can you know lung cancer is caused by smoking?

Van der steen:

1. Type one interferons. How are they used to treat disease? We saw two examples. Explain them both. On what mechanism do they work? In case of INF-beta, does it work better glycosylated or non-glycosylated and why?
2. A group of researchers want to make a small biological against sequestration of malaria. Why could such a drug be useful? We saw to types of drug screens. Describe the differences and (dis)advantages. When developping the anti-sequestration drug, would you go for an intracellular or extracellular target?

Lambrechts:

1. Give 2 examples of an inducible gene expression system. Describe them schematically.
2. Somatic copy number alterations are frequent in solid tumors. We discussed 2 examples of how these copy number alterations can be used as biomarkers: 1/ to tailor PARP inhibitors to ovarian cancer patients or 2/ to aid in the pre-symptomatic detection of cancer in pregnant women. Give the name of both genetic tests and briefly describe how they work (give their underlying principle).

09 January 2026

Lambrechts was present for the oral exam

Cools:

1. Explain PROTAC and molecular glues. Compare. Give an example in cancer-context. Which technique do you use for measuring if your PROTAC worked?
2. Explain 4 definitions/concepts
   • Bispecific antibodies
   • Effect deamination on mutations
   • Why does clonal hematopoiesis increase with aging
   • How can we change a transcriptional repressor into an activator

Lambrechts:

1. Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
2. Describe schematicaly how i) chemical and ii) transposon insertional mutagenesis screens work in zebrafish and explain. How would you use a CRISPR screen in the zebrafish (discuss the example highlighted) and would this result in comparable data as in i) and ii). Finally, describe which system you use to induce gene expression in the zebrafish.

Van den Steen:

1. difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
2. A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

09 January 2026 AM

Cools and Lambrechts were present for the oral exam

Cools:

1. Explain Clonal hematopoeisis (what it is). Why it is different from Leukemia. To what other disease/complications it is linked. Something about the expected VAF of CH.
2. Explain 4 definitions/concepts
   • PROTAC
   • mutation signature
   • CAR T-cell
   • How can we change a transcriptional repressor into an activator

Lambrechts:

1. Describe the Cre-recombinase system. Cre recombinase is used to generate 5 types of transgenic mice. Describe each type briefly.
2. Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types

Van den Steen:

1. What vaccination strategy should you use against leishamania polysaccharides, why do you think this would (not) be effective?
2. Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?

17 Januari 2025 AM

Van Den Steen and Lambrechts were present for the oral exam

Cools:

1. What is CAR T cell therapy? How can there be resistance against CAR T cell therapy? How can we improve the CAR T cell therapy to prevent resistance?
2. Explain 4 definitions/concepts
   • H3K4me3
   • Effect deamination on mutations
   • siRNAs
   • Irreversible kinase inhibitors

Lambrechts:

1. We discussed the usage of three model organisms. Can you describe their advantages and disadvantages that you would take into account when designing your laboratory experiments?
2. Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.

Van den Steen:

1. difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
2. monoclonal antibody (called malarimab) with high affinity for circum-sporozoite protein was designed: explain how this can be used in the fight against malaria - effector mechanisms, compare with vaccination and with antimalarial drugs chloroquine and artemisinine, how can there be optimisation of the monoclonal antibody and should the monoclonal antibody be sialylated to have good anti-malarial activity?

16 Januari 2025 PM

Cools and Lambrechts were present for the oral exam

Cools:

1. What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
2. Four questions:
   • What is the difference between bulk CRISPR screens and single cell CRISPR screens?
   • What is PROTAC?
   • What are CAR-T cells?
   • H3K27me3

Lambrechts:

1. Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?
2. After quality control , scRNAseq can be analyzed in different ways. Please describe some of the methods typically used to assess differences between 2 conditions by scRNAseq.

Van den Steen:

1. Explain artemisin, what is the difference with derivatives, how can resistance occur and how to combat resistance?
2. Develop a vaccine against specific saccharide of T. Cruzi. Which vaccine do you use, how to adapt it, what process is used and how can T. cruzi acquire resistance?

16 Januari 2025 AM

Oral exam by one of the professors (we had the oral exam from Lambrechts)

Cools:

1. Give the 3 ways to do immunotherapy on cancer cells, describe them, give their advantages and dis-
2. Explain 4 definitions/concepts
   • PROTAC
   • H3K4me3
   • ChIP seq
   • Clonal hematopoeisis

Lambrechts:

1. Question about somatic number mutations (PARP inhibitors etc)
2. Question about Cre recombinase and the 5 applications (transgenic mice)

Van den Steen

1. mRNA vaccin: explain design, mechanism and immunology of this concept
2. explain malaria sequestration, if you would use small molecule inhibitors and explain difference between phenotype and targetting screening and explain how you could use targetting screens.

10 Januari 2025 PM

You had an oral exam by one of the professors (post-it note on exam paper which one)

Cools (oral: he read your answer and asked extra questions, do not need to explain again what you wrote down):

1. What is CAR T cell therapy? How to detect if it worked (answer: PCR of TCR DNA)? What are some problems (at least 3) and how to solve these?
2. Four questions:
   • genome instability
   • PROTAC
   • ChIPseq
   • bivalent antibodies (bijvraag: advantages and disadvantages compared to CAR T)

Lambrechts:

1. scRNAseq can be complemented by CITEseq, scTCRseq and ATACseq. Can you explain how and what these 3 methods measure?
2. How is zygote injection used to generate transgenic mice ? Which are the 5 potential applications in brief ?

Van den Steen (oral):

1. difluoromethylornithine is a repurposed drug: mechanism(s), discovery process, other thing(s) used for
2. vaccination strategy against leishamania polysaccharides, why do you think this would (not) be effective?

10 Januari 2025 AM

Cools and Van den Steen were present for the oral exam Cools:

1. What is clonal hematopoiesis? How to detect it? What are the consequences/implications when it is detected?
2. Four questions:
   • What is the difference between bulk CRISPR screens and single cell CRISPR screens?
   • What is PROTAC?
   • What are CAR-T cells?
   • H3K27me3

Lambrechts:

1. Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
2. Can you (schematically) describe the technology used by the scientist Jiankee He. Can you describe what Jiankee He did to upset the international scientic community. And why is there less controversy around the authorised use of Casegevy in humans - describe ?

Van den Steen:

1. Give two examples of therapeutics of type 1 interferon. Also describe the underlying mechanism. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
2. A researcher wants to make a passive immunization therapy for placental malaria. What are the advantages/disadvantages of passive immunization and how does it work? What antigen should be targeted and explain in detail what it does/how it works. Should the antibody be sialylated? How can the antibodies be optimized? Would this therapy be effective? Why (not)?

6 september 2024

Cools:

1. Whole-exome sequencing data of white blood cells of individuals given including the VAF of the mutations. The mutations that were found were DNMT3A, JAK2, TET2 and ASXL1: what is going on in these individuals, what can you conclude from the data, what would you recommend these individuals?
2. Describe 3 different types of immunotherapy for cancer treatment in detail, compare these different types and give their advantages and disadvantages, also explain the main problems with these types of immunotherapy

Van Den Steen:

1. What are the biological therapeutics for TNF-alfa. Compare, give advantages and disadvantages. What is the main therapeutic that is used? What is the main problem with it? Would you sialylate this biological therapeutic?
2. Design a vaccination strategy against Trypanosoma cruzi

Lambrechts:

1. Two types of spatial transcriptomic technologies exist. Name them, describe their key differences and schematically illustrate an example of a method that was commercialized for each of both types.
2. Describe the principle of linkage disequilibrium between SNPs, and indicate in which studies this disequilibrium is being used. How do these studies work? We also discussed how SNPs are being used to predict risk of developing a disease, risk of developing side-effects in response to treatment or to identify the underlying mechanisms of disease. Can you briefly explain?

18 januari 2024

Cools:

1. what is clonal hematopoiesis? How to detect? Consequences/implications?
2. a) CAR-T cell b) single-cell CRISPR screen c) ATAC sequencing d) PROTAC

Van den Steen:

1. IFN-alfa: give the different types + their (dis)advantages, their application, should they be sialylated?
2. Explain placental malaria + which type of vaccine would you make + would it be effective?

Lambrechts:

1. PARP inhibitors and pre-symptomatic tumor detection; name of the two tests and how they work.
2. Cre recombinase system + 4 types of mouse models

12 januari 2024

Cools:

1. Ik heb 10 kankercellijnen waarvan er 4 een puntmutatie hebben op een non-coded region. De puntmutatie bevindt zich voor de promotor van een gekend oncogen. Hoe controleer ik of de puntmutatie invloed heeft op de expressie van dit oncogen? Beschrijf de methodes die je zou toepassen (ChIP sequencing + ATAC)
2. a) oncohistones b) single-cell CRISPR screen c) bispecific antibodies d) PROTAC

Van den Steen:

1. Give two examples of therapeutics of type 1 interferon. Should IFN-bèta be glycosylated when used as therapeutic? Explain why (not)
2. What is the link between sequestration and evading the immune system regarding malaria? Could the molecules used for sequestration be a good vaccin target? Explain in detail why (not).

Lambrechts:

1. What is measured with CITEseq, ATACseq and scTCRseq? Explain briefly
2. How is zygote injection done to generate a transgenic mice? Give briefly 5 examples.

19 januari 2023

Cools:

1. a) PROTAC b) Problems when using in cancer treatment
2. ChIP-sequencing
3. ShRNA screen against 100 genes of which 1 causing drug resistance
4. a) What is clonal hematopoiesis? b) 100 people, how do you find out who has CH? Describe step by step: what do you need/what technology do you use/how do you perform data analysis?

Eelen:

1. What is meant by 'Gene transfer in somatic cells'? Give an example. - max. 5 lines
2. How can the Cre/LoxP system be made inducible? Can it be made tissue specific? - max. 5 lines
3. Explain the Tet-on/Tet-off system schematically. Can it be made tissue specific? - max. 1 page

Lambrechts:

1. PRS? How did it originate? How can it be used for breast cancer?
2. Methylation as chemical marker? Chemical reaction? Use?

Van Den Steen:

1. Passive immunisation therapy against cerebral malaria
2. Difluoro-methylornithine