How DNA Fingerprinting Spots Gene Deletions in Mouse Tumours
Imagine cancer not as a single disease, but as a cellular crime spree where the instructions within our cells go rogue. At the heart of this mystery lies damaged DNA—genes that have been amplified, mutated, or entirely deleted. For decades, scientists have worked like forensic detectives to piece together what goes wrong in a cancer cell.
Among their most powerful tools is DNA fingerprinting, a technique that, much like human fingerprinting at a crime scene, can uniquely identify the genetic alterations specific to tumour cells. This article explores how researchers have adapted this ingenious method to detect a critical type of genetic damage in mouse tumours: gene deletions, some of which silence the very genes that normally protect us from cancer.
When you hear "DNA fingerprinting," you might think of crime scene investigations and paternity tests. In those fields, the technique distinguishes between individuals by looking at the unique patterns in their DNA. Scientists have cleverly repurposed this tool for cancer research. The goal is not to compare two individuals, but to compare healthy cells and tumour cells from the same organism.
If a gene is deleted in tumour cells, its "signal" will be missing or fainter when the tumour's DNA fingerprint is compared to that of normal tissue 1 .
Deletions are particularly dangerous when they affect tumour suppressor genes, the cell's natural defence mechanisms against uncontrolled growth.
While several methods can create a DNA fingerprint, one has been particularly pivotal for analysing genetic changes in cancer: Arbitrarily Primed PCR (AP-PCR) 1 . Let's break down this complex-sounding term.
Polymerase Chain Reaction acts like a DNA photocopier, making millions of copies of specific DNA sequences.
Uses short primers that bind to random, multiple sites across the entire genome 1 .
Deletions appear as missing or fainter bands, while amplified genes show up as stronger bands 1 .
Think of it this way: if the genome is a vast library of books, a targeted approach would pull out and examine one specific book. AP-PCR, however, takes a random sample of paragraphs from hundreds of different books all at once.
To understand how this works in practice, let's dive into a hypothetical but realistic experiment, built on the principles and discoveries from seminal DNA fingerprinting studies.
Researchers collect two types of tissue from a mouse model of cancer: a small piece of the tumour and a piece of healthy tissue to serve as a normal genetic reference 1 .
The genetic material (DNA) is carefully purified from both samples.
The DNA from both samples is subjected to AP-PCR. Short, arbitrary primers are added, and the PCR process runs, amplifying random fragments from across the genome 1 .
The banding patterns from the tumour and normal tissue are placed side-by-side and compared. A missing band in the tumour lane indicates a heterozygous deletion—the loss of one copy of a gene at that specific location 1 .
The most critical step is to identify which gene has been deleted. The missing band is cut out from the gel, and the DNA within is purified and sequenced to determine its exact genetic code and its location in the genome 1 .
In our simulated experiment, the AP-PCR fingerprint reveals several consistent deletions in the tumour samples. Sequencing one particularly prominent missing band shows that it originates from a region on mouse chromosome 11, a location known to harbour a powerful tumour suppressor gene called p53.
| Sample Type | Total Bands | Bands with Normal Intensity | Faint Bands (Deletions) | Strong Bands (Amplifications) |
|---|---|---|---|---|
| Healthy Tissue | 112 | 112 | 0 | 0 |
| Tumour A | 112 | 98 | 10 | 4 |
| Tumour B | 112 | 85 | 22 | 5 |
Loss of function, often of a tumour suppressor like p53
Over-activation of growth signals like c-Myc
Can subtly alter protein function like in KRAS
Studies have shown that mice with a higher GDF, indicating more widespread chromosomal damage, often have a poorer prognosis, mirroring findings in human cancers like gastric and colon cancer 1 .
Essential reagents and their functions in DNA fingerprinting experiments:
A special enzyme that can amplify DNA directly from crude cell lysates, speeding up the process 3 .
Short, random DNA sequences that initiate the amplification of random genomic sites 1 .
Used to purify and extract DNA fragments from gels after electrophoresis for sequencing 3 .
A small, circular DNA molecule that allows researchers to clone and amplify a specific DNA fragment for further analysis 3 .
Mouse models are used precisely because their biology closely mirrors our own. Finding a p53 deletion in a mouse tumour solidifies our understanding of its critical role as a "guardian of the genome" in humans.
Widespread deletions and amplifications are a hallmark of cancer cells, indicating a genome in chaos. AP-PCR helped reveal that tumours with a high degree of this damage (a high GDF) are often more aggressive, providing a potential prognostic indicator 1 .
DNA fingerprinting techniques like AP-PCR provided researchers with one of the first powerful, accessible tools to peer into the chaotic genome of a cancer cell without any preconceived notions. By applying this method to mouse tumours, scientists uncovered fundamental truths about how gene deletions drive cancer progression, paving the way for more sophisticated technologies.