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Yamanaka's and Sinclair's cellular reprogramming for the layman

HC Lee

2021 July 22

Response to a reader's query

This post is written in response to the wish of a reader of my post on Sinclair's "Lifespan" to know more about reprogramming. My knowledge in this field is superficial; I've never done any experiment. But I'll try my best to explain the concept involved, simply. Text enclosed in [...] gives more detailed explanation of some special terms; it can be skipped over in first reading.

What I wrote in the "Yamanaka and the reprogram of differentiated adult cell" section of my Sinclair's "Lifespan" post is indeed too cryptic an explanation for what reprogramming is about:

"Yamanaka showed that artificially importing four specific genes, now known as the four Yamanaka factors, which are normally locked in adult cells, into an adult cell triggers a process in which the cells would, over many divisions (as many as 60 generations), gradually fully unlock the epigenome, and this turns the cell into a stem cell that has the capability to differentiate into a variety of adult cells distinct from what it was before."

Yamanaka's cellular reprogramming

In the sense used by molecular biologists such as Yamanaka and Sinclair, the word program means the steps that epigenetics takes to control the genes on the genome (i.e., DNA) to affect cell differentiation. Cell programming leads to cellular differentiation, which, in human, begins to occur approximately in the three-week-old embryo. In completely differentiated cells, or adult cell, genes unneeded to carry out functions specific to the cell are locked up. Conversely, all genes that are not locked up are needed for those functions and can be, and will be, freely "expressed".

[Here, the expression of a gene, which codes a protein, means the reading and translation of the code and the building of the coded protein. Proteins are Nature's nano-machines; if we think of the cell as a giant plant, then the proteins are the supervisors/workers/switches/machines in the plant.]

The steps in the cell differentiation program are not all well understood, but it is believed genes are locked up in a complex, ordered and hierarchical fashion. In humans, this process takes nine months to complete its first phase, and then extends to the host?s early teens.

Reprogramming means going in a direction that is opposite to programming. That means unlocking some (or all) of the locked genes, in an order reverse to that during programming.

Before Yamanaka's 2006 work it was thought reprogramming was impossible. Yamanaka (and his coworkers) demonstrated that importing four crucial genes, called the four Yamanaka factors, into an adult human cell is sufficient to trigger its reprogramming. Reprogramming is a long process; it takes about sixty cell cycles of reprogramming to unlock (almost) all the locked genes, bringing the cell back to a state that is close to its embryonic state. At this state the cell is a stem cell, called an induced pluripotent stem cell (iPSC); it can be made to differentiate into a number of types (but unlike an embryonic cell, not all types) of cells different from what it was before reprogramming. For instance, an iPSC generated from an adult skin cell may differentiate into a nerve cell, a liver cell, and so on.

[Biologists use inactivated viruses to import genes into the host cell, such that it will be expressed there and cause the production of the coded proteins. This is done when the desired proteins, for whatever reason, are not naturally produced in the host cell. In the case of cell reprogramming, the four Yamanaka factors (genes) are presumably locked and cannot express themselves.]

[In Yamanaka's pioneering work the chances of success in reprogramming is small, about 1 in 1000. This is because after the four Yamanaka factors are imported into the host recipient cell the experiment mostly allows Nature to take its course. The recipient cell just "brews" and goes through cell cycles with the imported factors inside. Presumably, if by chance the genes are unlocked in the right order then the cell is restored to its unprogrammed state. I understand the chances of successful reprogramming is much greater now.]

[Why are the four genes Yamanaka used to trigger cell reprogramming called "factors"? That is because the four proteins these four genes code for belong to a special kind of protein called transcription factor (TF). Each function in a cell is carried out by a group, or network, of different proteins working in a coordinated fashion. This network is controlled by a boss protein, called a TF, which acts as a switch for the network. The network is inactive if the TF is "off", or is absent. A drug that aims to interrupt a (disease causing) cell function by suppressing the TF of that function is called an inhibitor.]

Sinclair's cellular reprogramming

We now come to the reprogramming in Sinclair's anti-aging work. The goal is entirely different from Yamanaka's. Yamanaka wants to reprogram an adult cell from a (specifically) locked state to an (almost entirely) unlocked state; that is, to change an adult cell to an iPSC. Sinclair wants to reprogram an OLD adult cell into a YOUTHFUL, adult cell; that is, a cell in a CORRECTLY locked state.

This implies that the gene locking patterns in an old (adult) cell and a youthful cell are different. Indeed, they are. Sinclair (and others) showed that altering the gene locking pattern of a cell causes the cell to age, and this process begins right after the cell reaches maturity, which in humans occurs in mid teenage. For most organs the degree of alteration is approximately proportional to the time after cell maturity. As a result, as a cell ages its gene locking pattern becomes less and less true, and increasingly it does what it is supposed to do less well, and sometimes does things (badly of course) that it is not supposed to do.

Sinclair hypothesizes that by restoring the altered gene locking pattern of an aged cell to its true, unaltered pattern is effectively returning the aged cell to its youthful state. For the restoration Sinclair uses Yamanaka's reprogramming method, with two variations: (1) only three of the four Yamanaka factors (the fourth factor tends to cause cancer) are imported into the cell, and (2) the reprogramming is not allowed to go all the way to unlock all genes, rather it is terminated when the true locking pattern of a youthful cell is achieved (verified by experiment). Sinclair achieved notable success with this approach.

[That this approach can be successful is quite surprising, because, presumably, aging alters the true gene locking pattern randomly, and restoring to an ordered state that is randomly broken is generally not possible. As far as I am aware, the (even limited) success of Sinclair's work is not understood.]

Cellular reprogramming and anti-aging

I should add that Sinclair's cellular reprogramming probably works only for "epigenetic" aging, not other types of aging, especially those caused by physical wear and tear. For instance, one would not expect reprogramming to reverse the aging of joints caused by movement and impact, nor of organs whose function involves much motion (at the bio-molecular level), including pumping action. The latter would include heart, lung, liver, kidney, etc. Perhaps this is why Sinclair so far has applied reprogramming to optical and nerve cells, whose functions do not involve motion, but are to transmit electromagnetic signals. Still, reprogramming might rejuvenate the epigenetic aging sustained by those parts of an organ not associated with motion, such as the SA (sinoatrial) node, or pacemaker, and the AV (atrioventricular) node of the heart, which control its electrical system. This suggests that cellular reprogramming could be a useful treatment of arrhythmia (thanks to Shiang Liu for a discussion on this subject).

Concerning organs, my guess is that eventually humans will learn to grow them, using stem cells.

© HC Lee, July 22, 2021, Taoyuan, Taiwan