Lecture Notes for April 1


Programmed Cell Death (renamed Apoptosis in 1972)

J.F.R. Kerr, A.H. Wyllie and A.R. Currie (1972). "Apoptosis: A basic biological phenomenon with wide-ranging implications in tissue kinetics" British Journal of Cancer, vol. 26 pages 239-257. PMCID: PMC2008650

The word apoptosis didn't become popular until after 1980, after which it gradually supplanted the completely synonymous term "Programmed Cell Death". This caused many to believe a new phenomenon had been discovered, rather that a long-known phenomenon being renamed. Hundreds of embryologists had been studying it for at least a century. But for 15 or 20 years, on-line searches only went back to around 1980, which distorted ideas about dates of discovery.

An excellent review paper (which might interest you, but is NOT assigned reading) is by Thomas G. Cotter (July 2009) Nature Reviews of Cancer vol. 9 pages 501 to 507. As he describes, the leading researcher in the field was Alfred Glucksman, until the 1970s, who coined the name "karyopycnosis" and advocated the (then unpopular, but true) concept that the same mechanism causes all the different phenomena that we now call apoptosis. The most important paper in the field was a long, much admired review paper published in 1950 or 51, for which I haven't yet been able to find a citation. Notice how on-line searches, although very helpful in most ways, greatly distort almost everybody's understanding of historical development of scientific topics. In this case, because proposal of a new name (apoptosis) coincided with the earliest papers to be cited, the new name has been interpreted as being a new discovery. If on line searches had gone back to 1950, apoptosis would either still be called programmed cell death (as it was the first 20 years I taught this course), or maybe "Karyopycnosis", and Glucksman would still be credited for the major discoveries in the field. Instead, credit goes to those who re-described Glucksman's observations under the new name "Apoptosis".

I thought students in this course might enjoy learning a little about these historical ("sociological?") aspects of scientific progress. Credit tends to go mostly to whoever is advocating an idea at the time when the majority finally accepts it. Renaming a phenomenon reinforces this human tendency. Time limits on computer citation searches reinforces this phenomenon, because readers assume that the first citations they can find must be the earliest discovery of any given phenomenon. Giving of famous prizes reinforces these same errors, and produces a perverted "star system" which monopolizes credit for popularizers of a phenomenon, instead of the actual discoverers. Sometimes they are the same people, usually they are not.


Necrosis is the proper term for cells that are somehow killed, by damage, by chemicals, by lack of oxygen, or any kind of harmful external treatments.

Apoptosis specifically means self-destruction of cells, which digest themselves from the inside out, by activation of pre-existing membranes, it is now known.

Specific Examples of apoptosis:

1) Self destruction of the tail of tadpoles.

2) Self destruction of the cells that were between gums and lips.

3) Self destruction of cells between the fingers (otherwise webbing, like duck feet).

4) Self destruction of cells in the human neck region, so as to produce narrowing.

5) Dozens of other examples in structural shaping of vertebrate bodies. (Including posterior & anterior "necrotic zones" that narrow limbs) (Notice these should apparently be renamed "apoptotic zones")

6) In the cell lineage of Caenorhabditis elegans, exactly 131 cells undergo programmed cell death (although the worms seem normal if this is prevented; they just have a lot of extra nerve cells)

7) Self destruction of half or more of segmental sensory and motor neurons. (Claimed to be those motor nerves which do not find a muscle to innervate?)

8) Self destruction of more than 98% of T and B Lymphocytes. (This is claimed to be how "anti-self" lymphocytes are weeded out.)

9) Self destruction of many or most virus infected cells, as a method to limit infection.

10) Believed to be how cancer chemotherapy actually kills cells. (i.e. By inducing them to self destruct, in contrast to killing them directly, as had long been assumed. (And which most people still assume.)

[Heck, "Most People" are still so out of date they think that cancer is caused by cells growing too fast.]
[Outdated fallacies are a (the?) major reason why almost zero progress is being made in cancer treatment.]

The biochemical mechanism of apoptosis (programmed cell death)

Special proteolytic enzymes are in the cytoplasm of almost all differentiated cell types (and developing embryonic cells).

These enzymes have been named "caspases". The origin of the name is Calcium-dependent, Aspartate-directed, lytic enzymes). Some caspases hydrolyze molecules other than protein. It is a rapidly expanding field.

Caspases are synthesized as an inactivated "pro-enzyme" state, like trypsinogen and pepsinogen. This means that part of the amino acid chain/ blocks the active site of the enzyme; But this block can be digested away from the active site, thereby activating the enzyme, which enables this active form of the enzyme to digest the blocking sequences of amino acids from other molecules of the proenzyme . This is a very strong positive feedback. It can digest an entire cell from the inside out in a few minutes.

Mammals have many different caspases, each coded by a different gene. Some of these have different specificities. C. elegans nematodes (fortunately) have only one single caspase gene (the ced-3 gene). The discovery of caspases by the study of mutant animals was made possible by this fact: that mutation of one gene was sufficient to prevent apoptosis.

Genetic analysis is very powerful, but you should realize that it has blind spots. One blind spot is that if a given function can be accomplished by any of 2 or 3 (much less 10 or 12) different independent proteins, then you will have trouble detecting mutations that change any one of their genes. Incidentally, another blind spot is that mutations that are lethal (especially at earlier stages) may not be detectable . If mutant organisms always die, how are you going to know they ever existed? Here is a method for sounding very intelligent in the question period of a research seminar about some kind of genetic analysis: ask the speaker how they can exclude the possibility of lethal mutants. Of course, depending on the seminar, this could also make you sound pretentious and foolish. But often, it's a good question. Another blind spot is that repetition of the same or very similar DNA sequences makes it impractical to discover that part of the DNA sequence. Repetition defeats the computer algorithms for lining up sequences. Often when the news says that the genome of an organism has been completely sequenced, the truth is that as much as 20% or more was too repetitive to be sequenced.

Part of the programmed self-destruction of cells is the rupture of the inner membrane of mitochondria. (That is the membrane that has the hydrogen ion gradient, and that holds in lots of cytochromes.) At first, the relation to mitochondria surprised researchers, most of whom spent two or 3 years denying it. Now it makes sense as a way of releasing highly reactive chemicals into the cytoplasm. It is normal for scientists to refuse to accept data that doesn't fit their preconceptions, and this was a good example.

A protein named bcl-2 serves to inhibit programmed cell death. It was discovered in human lymphoma cancer cells (the "follicular" variety of non-Hodgkins Lymphoma). Because they synthesize too much bcl-2 protein, they are inhibited from undergoing apoptosis. These lymphoma cells accumulate without limit, and eventually displace the normal bone marrow cells. Notice that this has nothing at all to do with the rate of mitosis or cell division. Nevertheless, one of the treatments is cyclophosphamide, a chemical related to mustard gas which selectively kills fast growing cells. If it weren't for the myth that cancer is caused by excessively high rates of growth, anti DNA and anti-mitotic chemotherapy probably wouldn't have been tried as treatments. Fortunately, they were tried, and they are quite effective in killing these slow-growing cancer cells. Nobody understands why. (Don't look a gift horse in the mouth.)

The basic science part of cancer research is very poorly done, in my opinion. They just try things at random. It doesn't attract the best people, and many of the researchers are only in it for the money. I hope some of you taking this course will go into this field and do better than the people who now dominate research on cancer. They hold back progress. You can do better.

In more than 90% of patients with follicular lymphoma, the over-production of bcl-2 results from chromosome breakage and rejoining ("translocation") between chromosomes 14 and 18, at locations that put the DNA coding for bcl-2 just "down-stream" of the promoter region of the gene for the heavy chain of antibodies. Thus, when a cell tries to make antibodies, it makes lots of bcl-2 protein instead.

Since the antibody proteins produced by B-lymphocytes have a binding site that is special to them, some very smart researchers tested the practicality of curing lymphomas by isolating their binding sites, and raising monoclonal antibodies that would specifically attack only cells with those binding sites. Of course, this required making a different monoclonal antibody for each patient. This is expensive. It cost as much as five thousand dollars per patient, just to produce the monoclonal antibody. Although this is a tiny fraction of the hundreds of thousands of dollars charged for drugs that are non-specific, and that don't produce cures, it was decided not to continue that approach. If you think this was an outrageous decision, join the club. Google "Coley's toxins" for another example of an actual cure for cancer being dropped by the establishment.

Some new anti-bcl-2 drugs are now being tried. We can hope for the best. But you should realize that the economic motivation to produce non-curative drugs (that patients have to keep on taking) is much stronger than the motivation to produce real cures. In general, economic motivations are the best way to decide how funds will be spent. Cancer research is an exception.


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