Wait… Why Are We Still Using Embryonic Stem Cells?

Have you ever wondered about the future of medicine? We’ve advanced so far but there are still diseases like Alzheimer’s that are without a cure! The answer to these problems may be stem cells.

Parmin Sedigh
14 min readDec 23, 2020


Credit: Lukiyanova Natalia/frenta/Shutterstock

1, 440,000

That’s one of the most conservative estimates for the number of people that could have their life changed with the help of stem cells, in the US alone. Just for context, that’s more than the population of Estonia!

This is because stem cells are incredibly helpful in studying human development, modelling diseases, developing drugs, transplanting cells (such as for cancer patients), regeneration of cells and organs, and even mental disease diagnosis. I could write another whole article about this but for now just know that stem cells are super duper important for the future of medicine!

Even though more and more research has been done on stem cells, there’s still one question (out of many) that researchers are still debating. Can induced pluripotent stem cells completely replace embryonic stem cells in research use? If most of the words in that sentence made no sense to you, don’t fret and keep reading! If you totally know what I’m talking about and just want to get to the juicy stuff, then skip to here. (Safari users: this may not work for you so just scroll to the “Digging Deeper” section!)

The Basics

What Even Are Stem Cells?

So glad you asked! Cells are the building blocks of life that help perform nearly every function in your body. Stem cells are a specific type of cells that must fit two criteria…

  1. They must be self-renewing, which means they can replicate infinitely under the right conditions
  2. They must be be able to differentiate into various cell types

The first criterion is pretty self-explanatory, but the second one can be a little harder to understand. Differentiation is the cell’s ability to turn into another cell type like a kidney cell or a blood cell. Stem cells are like a robot that’s yet to be programmed. Once the robot gets some sort of guidance, like a few lines of code, it can turn start completing more specific tasks. Just like stem cells when they differentiate!

But there are varying levels to what the cells can differentiate into, based on how many supposed lines of code they have. Some cells, those known as totipotent, can turn into any of the 200+ cell types. Think of these stem cells as a baby. They have barely made any decisions in life and can choose to go down any career path they want.

Pluripotent stem cells (or PSCs for short) are a little farther along, and the subject of this article. Remember our baby/totipotent stem cells from before? Well, they’re 10 years old now so they’ve made some decisions. This means that some career paths are now closed to them. PSCs can turn into any cell type except placental ones.

Last up, we have multipotent stem cells. They’re in high school and so they have a pretty general idea of what field they want to go into. Some want to go into the health sciences field while others prefer the performing arts. Some examples of multipotent stem cells include neural stem cells or haematopoietic (blood) stem cells. Note: these are what are known as adult stem cells or somatic stem cells and are found in the adult body!

Dr. Esteban Mazzoni, professor of Biology at New York University explains the process of differentiation exceptionally well in one of his lectures

One way to see differentiation is to imagine these as a series of binary choices. At every step of the way, the cells have to choose a path to become something at the expense of the possibility of becoming something else. [And each time the cell makes a decision] by definition, [it is getting] farther [away from] any other place that [it] could have gone.

This concept can be hard to grasp at first so I recommend checking out my video on the basics of stem cells down below!

What Are Embryonic Stem Cells?

Now that we’ve got the bare bone basics out of the way, let’s learn a bit more about the main stars of today’s show. One of them is the embryonic stem cell or ESC as I’ll be referring to from now on.

ESCs are a type of pluripotent stem cell and they’re derived from embryos as you might have guessed but let’s go through the process in more detail!

Most ESCs come from a procedure called In Vitro Fertilization or IVF for short. IVF is usually done for infertile couples where the mature eggs of a woman are retrieved and then fertilized in vitro, or in a petri dish. They are then kept in a medium for a 3–6 days. At around day 5 or 6, the embryo reaches a stage called the blastocyst stage. This is our key stage because it’s when embryonic stem cells are retrieved.

The blastocyst has two main parts:

  1. Inner Cell Mass: often shortened to ICM, this is the part that then grows into the embryo
  2. Outer Layer: made of cells called trophoblasts which eventually give rise to the placenta
This is what a blastocyst looks like. Created by me and inspired from slides by Dr. Esteban Mazzoni

Embryonic stem cells come from the ICM. “But wait, didn’t you just say that’s the part that grows into the embryo and then the baby? Isn’t that unethical?” I hear you saying. I’m glad you’re paying attention, but the ethical battle can get complicated.

First off, it’s important to make it clear: good, healthy embryos are NOT used for the retrieval of ESCs. It is only those that are not as high quality or have been screened due to the parents having some sort of genetic mutation. And of course, there is always consent from the parents.

But that’s still doesn’t ease some people’s concerns. Plus, when ESCs are used for transplants, for example, there’s a high chance of rejection from the patient’s body because those are not their own cells. That’s where these amazing feats of science called induced pluripotent stem cells come in!

What Are Induced Pluripotent Stem Cells?

These stem cells, often referred to as iPSCs for short, were first discovered by Shinya Yamanaka in 2006. He was able to reprogram mature cells in mice back to immature stem cells, or what we now know are called pluripotent stem cells.

He was able to do this using four factors which are now known as the Yamanaka factors. You don’t need to remember this but it’s good to know what the four factors are: OCT 4, SOX 2, C-MYC, KLF 4.

Just to reiterate how amazing this discovery was, Yamanaka found a way to take adult stem cells, which are multipotent and don’t have much potential for differentiating, and turn them back into embryonic-like stem cells! That’s crazy cool!

A simplified version of how iPSCs work. Again created by yours truly!

But it’s that pesky little word that we’ll focus the rest of the article on: embryonic-like. When learning about both ESCs and iPSCs, I kept coming back to the same question.

If we’re able to create these iPSCs, then why don’t we stop using ESCs?

This will ensure that no one gets upset about the ethical questions surrounding the destruction of embryos and it also means we’ll never really run out of sources for our stem cell research since the number of people willing to get a simple biopsy of their skin is much higher than those willing to donate their excess blastocysts.

Turns out there’s a bunch of scientists and researchers that are working on figuring out what makes these two cell types so similar but also different. Let’s explore all of this together!

Digging Deeper

So now we know what stem cells are, what ESCs are, and what iPSCs are. Let’s dig into the nitty gritty and figure out what makes ESCs and iPSCs different so that we can find out why we haven’t eliminated the use of ESCs altogether!

Epigenetic Memory

Something very interesting is that several studies found the differences between iPSCs and ESCs to be almost entirely based on the epigenome and not the genome or DNA itself. You can think of the genome as a recipe. The epigenome would then be the actual cooking process.

For example, when you’re baking a cake, the recipe would call for some flour, sugar, baking powder, salt, butter, and eggs. The cooking process would be where the ingredients are put together, mixed, and then baked!

Turns out, iPSCs sometimes retain epigenetic memory of the original tissue they came from. This means they remembered the procedure that was used in their tissue of origin!

Left column = iPSCs derived from other sources. Right column = fibroblast-derived iPSCs. Alizarin red staining (a marker of osteogenic cells) was used.

One experiment tested this theory using iPSCs that were derived from fibroblasts. A fibroblast is “a specific type of connective tissue cell that is found in skin and tendons and other tough tissues in the body” according to genome.gov. Guess what? Researchers found that iPSCs derived from other sources as well as ESCs formed significantly less defined osteogenic (bone-related) colonies! What’s more the fibroblast-derived iPSCs also deposited more elemental calcium. As you might recall from elementary school, we have lots of calcium in our bones!

But what did the experiment show? It showed that the fibroblast-derived iPSCs retained memory of what type of cell they used to be. This could be useful in some instances, but if you’re trying to make the cell exactly like an ESC, then you’ve got a problem.

Different Methylation Patterns

Methylation patterns are very closely related to our epigenome. It is where methyl groups–groups of 1 carbon and 3 hydrogens–are added to our DNA.

Methylation doesn’t change the structure of DNA but it does repress gene transcription. Let’s go back to our cake analogy now! Remember how the epigenome is the cooking process and the DNA the recipe. Methylation is like baking the cake before mixing up the ingredients. The recipe’s still the same but since the ingredients weren’t mixed, ingredients like baking powder are “repressed”. It’s not a perfect analogy but it helps simplify things.

What does this have to do with stem cells again? Well, it’s been found that iPSCs do share some methylation patterns (that is where the DNA is methylated) with their ESC counterparts. These patterns are actually distinctly different from the patterns we see in adult stem cells. So we’re all good, right? Not quite.

Something else that researchers noticed was how iPSCs transmit their methylated areas to the differentiated cells that come after them more frequently than ESCs. iPSCs also exhibited signs of having specific methylation patterns, dissimilar ESCs. Lastly, these patterns actually indicated some form of epigenetic memory like we talked about above!

iPSCs Unnecessarily Undergo Apoptosis

When it comes to blast cells, which are the precursors to the mature, circulating blood cells, researchers observed that iPSCs underwent unnecessary apoptosis compared to ESCs. Think of apoptosis as a fairly peaceful, expected death of a cell. It’s often called programmed cell death and it occurs due to some genetic changes. It’s necessary to keep our bodies healthy but an excess of it is actually thought to be the cause of some diseases.

We’re gonna get a little technical now but bear with me! In order for cells to undergo apoptosis, we have something called a protease (an enzyme), and this specific one is caspase-3. It’s in the cell but it’s inactive when it’s just going about its business, not undergoing apoptosis. Whenever apoptosis is needed though, caspase-3 is cleaved by caspase-8 and caspase-9.

Time for another analogy! Capase-3 is a bad memory that you’ve managed to supress. Caspase-8 and caspase-9 are triggers that remind you of that bad memory. As long as they’re not present, that memory will stay suppressed.

Take a look at this! As you can probably guess, the bottom row represents cells derived from iPSCs while the top is from ESCs.

Now we get to the interesting part! More than 20% of the blast cells that were derived from iPSCs had cleaved caspase-3; the memory had been triggered. On the other hand, less than 1% of those derived from ESCs had cleaved caspase-3. Hence the conclusion: way more iPSCs undergo apoptosis unnecessarily!

Early Senescence

I won’t go into too much detail about what senescence is here, so feel free to check out my other video about human longevity that talks about senescence here!

To put it simply, senescent cells are like zombies. They’ve reached a stage where it’s dangerous for them to continue proliferating (or multiplying) so they “die”. But they don’t undergo apoptosis; instead, they’re left in a zombie-like state where they don’t do much other than take up space, cause inflammation, and more. (They do have some benefits but that’s beyond the scope of this article so click here to learn more.)

In short, you do not want to have cells be turning senescent too early. Unfortunately, that’s exactly what several studies have found to be true for iPSCs.

Blue indicates the presence of β-galactosidase (observe how the iPSCs show much more blue colouration!)

In one experiment with endothelial cells, more than 50% of the iPSCs expressed β-galactosidase, which has been shown to be a marker of senescence. This is while less than 5% of endothelial cells derived from ESCs exhibited that same marker.

Another experiment worked with retinal pigment epithelium cells or RPE for short. At first when the iPSCs and ESCs were differentiating into RPEs, they appeared to be acting quite similarly. However, as time went on, it became apparent how ESCs were growing robustly even after 2 or 3 passages. On the complete opposite side, iPSCs sometimes failed to even fill the first plate.

RPE cells at passage 2 stained with β-galactosidase. Just look at how much more stained the iPSCs are!

What does all that mean? Passaging is when the cells are transferred from one dish to another. Think of it like this: the iPSCs and ESCs are students. Each passage is equivalent to switching schools. ESCs are social and easily keep growing after a few times of switching schools. But iPSCs have trouble growing even at their initial school! What’s more, they also exhibited β-galactosidase, our best friend from before that’s an indicator of senescence!

Slow and Inconsistent Differentiation In Vivo

When both human iPSCs and human ESCs were injected into immunodeficient mice, both were able to result in proper teratoma growth. According to cancer.gov, teratomas are “a type of germ cell tumour that may contain several different types of tissue, such as hair, muscle, and bone.” However, those teratomas that came from iPSCs showed significantly slower growth. This suggested that iPSCs exhibit slower differentiation in vivo, or in a live animal.

iPSCs and ESCs were also compared for cardiomyocyte differentiation. Cardiomyocytes are responsible for the contractile force in the heart. When using ESCs, 27.0% ± 3.6% of the cell aggregates contained beating cardiomyocytes. On the other hand, when using iPSCs, only 11.2% ± 11.5% of the cell aggregates contained beating cardiomyocytes. This once again exhibits the iPSCs’ limited ability to differentiate compared to ESCs. Watch the video to see the cardiomyocytes beat; it’s amazing to see!

Let’s look at one more experiment to confirm the findings! This time we’re looking at endothelial cells. ESCs were able to demonstrate great in vitro expansion, that’s in a lab, at 85.3% ± 6.32%. However, iPSCs demonstrated limited expansion which actually suggests early senescence (as we discussed above!) iPSCs were at 28.2% ± 8.77% at the same time.

Reduced Pluripotency: The Dlk1-Dio3 Region

This very well ties into the previous point about a lack of differentiation but here we’ll be talking about a gene that was an indicator of how iPSCs are actually less pluripotent than ESCs, meaning they’re not the best at differentiating.

Now we’re gonna talk about the scary thing in the subtitle, the Dlk1-Dio3 region, which is a region in the genome! Scientists have found that this region is actively expressed in fully pluripotent stem cells and not in partially pluripotent ones.

Not all iPSC lines are actually partially pluripotent but some are. It’s not quite clear exactly which ones (based on my research) but we can use analysis of the Dlk1-Dio3 region to “screen” cells for pluripotency!

Not All Hope Is Lost

We just talked a lot about how iPSCs are different from ESCs so does this mean we’ll never be able to replace the use of ESCs with iPSCs or that iPSCs will never be used in clinical settings? Absolutely not!

I’ll be writing another article soon about the new advancements in iPSCs and their promising future. Until then feel free to check out this short article with a contrarian point of view, talking about how iPSCS = ESCs!


  • Stem cells are a specific type of cells that must fit two criteria: they must be self-renewing, they must be be able to differentiate
  • There are 3 main categories of stem cells: totipotent (can differentiate into any cell type), pluripotent (can differentiate into any cell type except placental ones), and multipotent (can differentiate into a cells group, like kidney cells)
  • Embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) are both pluripotent
  • ESCs come from in vitro fertilization, specifically the inner cell mass in the blastocyst (the stage of a fertilized egg after 5 or 6 days)
  • iPSCs are adult stem cells that are turned back into an embryonic-like state using the 4 Yamanaka factors: OCT 4, SOX 2, C-MYC, KLF 4
  • Since ESCs come from embryos they pose some ethical questions and they might be harder to use for transplants or other clinical techniques because the patient might reject thim. This wouldn’t be an issue with iPSCs
  • Unfortunately, iPSCs have some fairly significant differences compared to ESCs, which are the standard for pluripotent stem cell research including: epigenetic memory, different methylation patterns, unnecessary apoptosis, early senescence, slow and inconsistent differentiation, and reduced pluripotency

Hey there 👋 Parmin here; I’m a 15 y/o student studying stem cells at The Knowledge Society 🧪 Everyday, I aspire to uncover the secrets of biology and learn something new! Make sure to follow me on Medium to hear about every new article I post, connect with me on LinkedIn, or contact me at parminsedigh@gmail.com! Also subscribe to my monthly newsletter to learn about every cool, new thing I’m working on ✍️



Parmin Sedigh

Science communicator trying to learn something new everyday | Published in Start It Up, Predict & The Writing Cooperative