Biomarker Identification of Glioma in the CSF
A step-by-step guide on how to find biomarkers for Glioma within the CSF using Galaxy
Here is the video tutorial + explanation that goes along with this article:
There are three main sections for this tutorial:
- Biomarker application in cancer: what cancer is, how it progresses, how biomarkers can be a solution to cancer
- Introduction to glioma: what a glioma is, how there have been traces of glioma in the CSF + a study in which this has been found
- Using Galaxy to find glioma biomarkers within the body: a tutorial to use Galaxy — software used by professionals — to find biomarkers/traces of glioma
If you would like to jump straight to the tutorial, scroll down!
Biomarker application in cancer
Genetic mutations are great — they have helped us become a species through evolution. However, there are some dangerous and horrible ones — one of them being cancer.
Cancer has affected almost every one of us through a friend or family member. Cancer is, unfortunately, quite common in our society. In 2020 alone there were an estimated 18.1 million new cases of cancer. Even on a personal level, my family has experienced many triumphs and tragedies of cancer.
Through this article, I aim to provide a solution to cancer through biomarkers. But before we dive into the solution, let’s understand what cancer exactly is and how it occurs.
How Cancer Starts
Your body makes new cells almost all the time — about 330 million of them a day. Because of the sheer number of cells, there is sometimes an error during the process of replicating cells called a genetic mutation.
However, if the body does not catch this mistake and does not through apoptosis (cell suicide) this mutation can lead to a tumour. Above there is a diagram showing how cancer occurs.
The tumours can be formed in two ways:
- Benign tumours: These tumours just stay in one place. They don’t really do anything dangerous to the body and aren’t as urgent
- Malignant tumours: Now these are the ones you should worry about as they are cancerous! They can spread to different parts of the body and are dangerous to the body as they form its own blood vessel and invades the surrounding cells
Both of these tumours look very different and are in varying degrees of urgency.
A solution to cancer — Biomarkers
The truth is that cancer is quite a hard issue to tackle, as each tumour is a genetic mutation specific to the patient.
The current solutions include taking chemotherapy, hormone therapy, immunotherapy, stem cell transplant, surgery and targeted therapy.
However doctors have been researching a new way to treat cancer biomarkers.
Biomarker testing is a way to look for genes, proteins, and other substances that can provide information about cancer.
Once biomarker testing is completed, doctors are able to select the correct treatment for the patient. Some current solutions like immunotherapy (amplifying the bodies existing ability to fight viruses to fight cancer in the body) or targeted therapy (using antibodies to fight cancer) are based on the data found after completing the biomarker testing.
Introduction to Glioma
Some definitions:
Glioma: a growth of cells that starts in the brain or spinal cord — they look similar to glial cells (healthy brain cells ).
CSF/Cerebrospinal Fluid: The fluid that surrounds the brain cavity. It helps make the brain weigh less (since it is fluid)& allows it to be cushioned & provides nutrients.
Proteomic: Biomarkers that are proteins found in the body
Glioma is one of the least common cancers in the world — as well as one that is quite hard to locate. And the worst part of it is that it is almost always fatal.
To find and diagnose Glioma, doctors usually make patients go through imaging scans — most commonly MRI scans. However, the problem with this is that it is quite expensive (around $575 — $1,450 in Ontario) so many times patients are only able to know that they have the disease later on in their stages.
So, using biomarkers we might be able to better understand ways and potentially use them to detect glioma much faster than MRI scans.
A solution to this problem:
Through many research papers, I discovered that Glioma can actually be found through the CSF (Cerebrospinal fluid)!
The reason for this is many brain tumour cells shed (since these are malignant) and spread — the glioma cells move into the CSF.
An example of the research done is by Fatima et. al in 2008, there have been biomarkers of glioma found within the Cerebrospinal fluid (CSF).
You can read more about this here:
Their findings are that:
- They have found 21 proteomic biomarkers through various testing from Astrocytoma (a type of Glioma) patients
- The biomarkers differ based on the Grade of tumour in their body (Grade I would not have the same biomarker as Grade II), making biomarker testing even more difficult.
- The biomarkers could be a cause of a variety of reasons. They give some main reasons: a response to therapy, tumour recurrence, progression and prediction of tumour transformation to a higher grade
Using this same information, I created a system to identify these biomarkers similarly using computational software. Now let’s move on to the tutorial ;)
Using Galaxy to find glioma biomarkers within the body
Now onto how we can find potential biomarkers, here are the steps I took to find them ⬇️
As a quick introduction, I used Galaxy Computational Software to find these biomarkers. In a nutshell, Galaxy is a tool to find specific medical information (like biomarkers in this case) using filters to find the specific information you want.
I found it quite similar to Scratch, with building blocks that you could use to go through the information.
Before starting the tutorial, I would suggest skimming through this training course on galaxy: https://training.galaxyproject.org/
#1 Opening an account
The website I used for this is https://proteore.org/. I found this website much easier to use then any other I have gone through.
#2 Create new workflow
Clicking on the + icon in the top right corner, create a new workflow. Rename it to “Glioma Biomarker Identification”.
#3 Enter the workflow and select the type of Cancer
Once you have entered the workflow, search for “Get expression profiles”. Now, edit the module so that you select the “Human Tumor Tissue” from the Human Protein Atlas database.
Now finally, select the “glioma”. Now we have found many types of genes that are linked to this type of Cancer.
However, not all of these genes are prognostically favourable — something essential for this diagnostic as they would not provide any evidence if the tumor is present.
#4 Filter through to only select the prognostic genes
Now, we must filter through the remaining genes that are not prognostically favourable, and have only the ones that are. As shown in the screenshot, I apply the discarded filter to the “c8” column and discard the ones that have “NA” in that column.
#4 Filter through to only select the datasets that are found within the CSF
It is much easier to access the CSF than the patients brain. Therefore, I chose to filter through to only use the genes that are found within the CSF.
#5 Final dataset!
Now we have finally found some genes that are linked to glioma, both prognostically favourable and found in the CSF! With these biomarkers, researchers are able to link this cancer to other causes, hopefully being able to find a cure in the future.
You can follow along with my published workflow here ⬇️
Hey! Thanks for reading my article! It means a lot to me!!
My name is Anya Ishani Sharma, and I am a grade 11 student passionate about biotech! If you loved this article and would like to discuss it with me please feel free to reach out. You can contact me through my email (anya.ishani.sharma@gmail.com), and my Linkedin (click here).
