Breast cancer is one of the most common cancers worldwide.
Scientists Used Computers to Crack Breast Cancer’s Hidden Code
Bioinformatics in cancer research
Breast cancer is one of the most common cancers worldwide. Every year, millions of women face this disease. Scientists keep searching for better ways to detect and treat it. At first, most research focused on genes that control cell growth. After that, scientists began looking at something deeper. They started studying epigenetics — how genes are switched on or off without changing the DNA itself.
A brand new study published in Discover Biotechnology takes this idea further. Mirzaei et al. (2026) used powerful computer tools to study a gene family called lysine demethylases (KDMs). These genes act like volume knobs on your DNA. They control how loud or quiet a gene is. To put it differently, they remove tiny chemical tags called methyl groups from histone proteins. Histones are like spools that DNA wraps around. As a result, when KDMs remove those tags, it changes which genes are active in a cancer cell.
All in all, this study used nine different online databases. The researchers analyzed data from hundreds of breast cancer patients. The goal was to answer one key question: Can KDM genes help doctors predict and treat breast cancer better?
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How Did the Scientists Do This?
They Used Free, Public Online Tools
To enumerate, the research team used a whole toolkit of free databases:
- UALCAN — to check how active KDM genes are in tumors vs. normal tissue
- Kaplan-Meier Plotter — to see if KDM gene levels affect patient survival
- cBioPortal — to find mutations and copy number changes in KDM genes
- STRING and Cytoscape — to map how KDM proteins interact with each other
- GSCALite — to see how KDMs relate to drug sensitivity
- TIMER — to study how KDMs affect the immune system inside tumors
At this point, you might be wondering: why use so many tools? Seeing that breast cancer is complex, no single tool gives the full picture. So as to get reliable results, combining all these databases makes the findings much stronger.
They Studied Over 1,000 Patient Samples
The team analyzed data from the TCGA (The Cancer Genome Atlas) database. This included over 1,100 breast cancer samples. Prior to this kind of study, scientists had to run expensive lab experiments. At the present time, tools like TCGA let researchers study human data at scale — using only a computer.
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Bioinformatics in cancer research: What Did They Find?
KDM Genes Are Misregulated in Breast Cancer
The research found something fascinating. Several KDM genes were much more active in tumor tissue. For example, KDM5B was turned up high in many breast cancers. What’s more, patients with high KDM5B levels had shorter survival times. In contrast, some other KDM genes — like KDM6A and KDM4B — were low in tumors. When those genes were higher, patients actually lived longer.
To illustrate, think of it like a classroom. Some students (genes) are overachievers causing chaos. Others are the calming influence. In breast cancer, the balance is broken.
KDM2B and Drug Resistance
One of the most exciting findings involves KDM2B. This gene showed the strongest links to how cancer cells respond to drugs. The study found that high KDM2B expression was linked to resistance to Methotrexate and Doxorubicin — two common chemotherapy drugs. So long as KDM2B stays highly active, cancer cells seem to fight off treatment.
At least five thousand drugs were analyzed for their connection to KDM genes. This is a massive amount of data. Provided that future experiments confirm these findings, KDM2B could become a key target for new cancer treatments.
The Immune System Connection
While it may be true that most cancer research focuses on genes alone, this study went further. The team also studied the tumor microenvironment — the mix of immune cells surrounding a tumor. KDM5A, for example, showed a strong positive link with CD8+ T cells. These are the “killer” immune cells that attack cancer. With this in mind, boosting certain KDM genes might help the immune system fight breast cancer more effectively.
Why Does This Matter for You as a Student?
This Is Exactly What Bioinformatics Scientists Do
So far, most people think of scientists as working only in wet labs with test tubes. But this entire study was done using a laptop and free online databases. No lab coat needed! As a matter of fact, this is a fast-growing career field called bioinformatics – and it is wide open for the next generation of STEM students.
If you love biology AND data AND computers, this is your field. You should read more about why study data science on ENTECH Online. Data skills are the backbone of modern biology research.
STEM Career Paths: Bioinformatics in cancer research
All things considered, this one paper touches on careers across multiple STEM fields:
- Bioinformatician — analyzing genomic data using Python, R, and statistics
- Cancer research scientist — studying how genes drive disease
- Pharmacogenomics specialist — matching drugs to a patient’s genetic profile
- Computational biologist — building models to predict how tumors behave
- Immunologist — studying how the immune system responds to cancer
- Clinical data scientist — using patient data to improve treatments
What’s more, you can start building these skills now. Learning tools like R or Python in high school gives you a strong head start. Working with free platforms like UALCAN or TCGA is also possible for curious students. Also, check out ENTECH Online’s article on biological classification – because understanding life’s organization is where all biology careers begin.
Reference:
- Mirzaei, Z., Barati, T., Ebrahimi, A., & Shekari Khaniani, M. (2026). Integrated bioinformatics profiling of the lysine demethylase gene family in breast cancer. Discover Biotechnology, 3, Article 9. https://doi.org/10.1007/s44340-026-00055-0
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