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BMS3031 - Molecular mechanisms of disease - S1 2026

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A researcher is testing an

antisense

oligonucleotide (ASO)

designed to reduce the expression of a

disease-causing protein. After treatment, the level of the

target mRNA decreases significantly

, and

as a result, much less of the protein is produced.

Which mechanism most likely explains how the ASO

produced this effect?

The

ASO forms complexes with cellular proteases that degrade the translated protein

❌

The

ASO blocks RNA polymerase from binding to the gene promoter

❌

The

ASO binds to the target mRNA and recruits

RNase H

, which degrades the RNA

strand

✅

The

ASO blocks mRNA binding to the ribosome through steric hinderance

❌

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A woman

carries a

pathogenic mutation in her mitochondrial DNA

, creating a high

risk of transmitting mitochondrial disease to her children. She and her partner

want a child that:

inherits their nuclear
DNA
, but

does not inherit the
mother’s mutated mitochondria
.

clinician proposes

mitochondrial replacement therapy

to achieve this

outcome.

Which

procedure would best meet the couple’s goal?

Transfer

of mitochondria from the father’s sperm into the mother’s egg to replace the

mother’s mitochondria

❌

Use

mitochondrial editing to repair the mother’s mitochondrial DNA, prior to

fertilisation of the egg

❌

Transfer

the nucleus from the parents’ fertilised egg into a donor egg that contains

healthy mitochondria but has had its nucleus removed

✅

Use

gene editing to repair the mitochondrial DNA mutation inside the embryo

❌

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A researcher wants to introduce a

targeted

double-strand break in DNA

to stimulate genome editing in human cells.

They are considering several programmable gene-editing technologies and need to

choose one capable of generating this type of DNA damage.

Which conclusion best reflects the capabilities

of the available tools?

Only

CRISPR–Cas9 can generate targeted double-strand DNA breaks in cells

❌

Double-strand

DNA breaks cannot be precisely engineered within dividing cells

❌

Zinc

Finger Nucleases, TALENs, and CRISPR–Cas9 can all be engineered to create

targeted double-strand breaks in DNA.

✅

Zinc

Finger Nucleases and TALENs can generate double-strand breaks, but CRISPR–Cas9

cannot

❌

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Researchers are developing an antisense oligonucleotide (ASO) therapy

for a patient with

Duchenne muscular dystrophy (DMD)

who has a deletion of

exon 52 in the dystrophin

gene. This deletion disrupts the reading frame,

preventing production of a functional dystrophin protein.

To address this, the therapy is designed to

cause

exons 52 & 53 to be skipped during mRNA splicing.

Why could this strategy restore dystrophin function?

Skipping

exons 52 & 53 restores the correct reading frame of the mRNA, allowing

production of a shorter but functional dystrophin protein

✅

Skipping

exon 52 & 53 increases the stability of dystrophin by removing an unstable

protein domain

❌

Skipping

exons 52 & 53 restores dystrophin to its original wildtype length

❌

Skipping

exons 52 & 53 removes all mutations present in the dystrophin gene

❌

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A research team is developing a

CRISPR-Cas9

therapy for sickle cell disease

using a patient’s haematopoietic stem

cells. Instead of trying to directly fix the mutated β-globin gene, they design

a strategy that edits a

regulatory region
controlling haemoglobin expression

. After editing, patients begin

producing high levels of

fetal haemoglobin

(HbF)

, which compensates for the defective adult β-globin.

Which gene-editing strategy best explains how

this therapy works?

Inserting

an additional functional β-globin gene into haematopoietic stem cells using

CRISPR-mediated recombination

❌

Repairing

the regulatory enhancer controlling BCL11A using HDR to restore normal β-globin

expression

❌

Disrupting

the BCL11A erythroid enhancer in haematopoietic stem cells using non-homologous

end joining (NHEJ), allowing fetal haemoglobin expression

✅

Precisely

correcting the mutated β-globin gene sequence using homology-directed repair

(HDR)

❌

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Researchers are attempting to correct a disease-causing mutation using

CRISPR in mature neurons taken from an adult patient. They plan to use

homology-directed repair (HDR)

with a

donor DNA template to precisely replace the faulty sequence.

However, the experiment produces very few

successfully edited cells.

What is the

most

likely explanation

for the poor editing efficiency?

HDR

repair mechanisms operate inefficiently in cells that are not actively dividing

✅

Donor

DNA templates cannot integrate into human cells

❌

HDR

requires meiotic cell division to function correctly

❌

The

guide RNA cannot locate a sufficiently unique DNA target sequence in neuronal

DNA

❌

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Duchenne Muscular dystrophy (DMD) can be caused by a mutation leading to the exclusion of exons 49 and 50 of the dystrophin gene (exon pattern illustrated below).

Which of the following proposed antisense oligonucleotide (ASO) treatment would likely be most effective for patients with this mutation, to allow them to produce some functional dystrophin protein?

DMD patient exon pattern

A antisense oligonucleotide therapy that results in skipping of exon 51

✅

A antisense oligonucleotide therapy that results in skipping of exon 51 & 52

❌

A antisense oligonucleotide therapy that results in skipping of exon 47 & 48

❌

A antisense oligonucleotide therapy that results in skipping of exon 48, 51 & 52

❌

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A 32-year-old patient with HIV is enrolled in a clinical

trial for an experimental therapy aimed at making their T cells resistant to

viral entry. The therapy targets the CCR5 co-receptor, which HIV uses to infect

T cells. The research team must decide how to deliver the zinc finger nucleases

(ZFNs) to safely and effectively disrupt CCR5 in the patient’s cells.

Which delivery strategy was used in this type of

CCR5-targeted ZFN therapy?

Direct

intravenous administration of ZFN proteins to target the patient’s T cells

❌

Intravenous

delivery of a viral vector encoding ZFNs directly to the patient’s T cells

❌

vivo treatment of the patient’s T cells with ZFNs, followed by reinfusion of

the edited cells

✅

vivo treatment of the patient’s T cells with ZFNs, followed by reinfusion of

the edited cells

❌

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A woman carries a pathogenic mutation in her mitochondrial

DNA that places any biological child at high risk of developing a severe,

early-onset mitochondrial disorder. She and her partner seek a reproductive

option that allows them to have a genetically related child while minimising

the risk of disease transmission.

In this context, what is the primary therapeutic purpose of

mitochondrial donation (mitochondrial replacement therapy)?

replace defective mitochondria inherited from either parent with healthy donor

mitochondria

❌

correct nuclear gene variants associated with mitochondrial disease

❌

treat mitochondrial dysfunction in the mother prior to conception

❌

prevent transmission of pathogenic mitochondria inherited exclusively from the

mother

✅

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Leber congenital amaurosis caused by RPE65 deficiency leads

to progressive retinal dystrophy due to impaired regeneration of 11-cis-retinal

in photoreceptor cells. Luxturna is an AAV-based gene therapy designed to

restore visual function in affected patients.

Clinical studies show sustained RPE65 expression and

improved vision for years after a single subretinal injection, despite the

absence of targeted genome editing.

Which property of the Luxturna AAV vector best explains this

long-term therapeutic effect?

Correction

of the defective RPE65 gene through non-homologous end joining

❌

Persistence

of the therapeutic RPE65 transgene as an episomal DNA element which is

integrated into the genome

❌

Correction

of the defective RPE65 gene through homologous recombination

❌

Persistence

of the therapeutic RPE65 transgene as an episomal DNA element in the nucleus

✅

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