The war on DNA

ve been reading a recent book titled Targeting the DNA Damage Response for Anti-Cancer Therapy, edited by J Pollard and N Curtin. I don't recommend this for the general reader: you practically need a degree in molecular biology to understand it. Also, there's no index and no table of acronyms. But it's wonderfully written and stuffed with useful facts about the DNA damage response, which is becoming a hot topic in brain science. What's shocking is that oncologists are targeting the same molecular pathways that neurologists are targeting. The difference is that oncologists are trying to kill cells while everyone else is trying to keep cells alive.

How a bombing in WWII led to a cancer treatment

On December 2, 1943, the Luftwaffe bombed an Allied fleet in Bari, Italy, killing over a thousand allied troops. Historians call it Little Pearl Harbor. One of the ships, the John Harvey, was carrying a number of 100-pound bombs filled with mustard gas, known as sulfur mustard, because it was feared that the Germans might resort to chemical warfare.

Doctors found that the 83 who died from mustard gas exposure showed a loss of white cells, or leukocytes, causing leukopenia. Military doctors theorized that nitrogen mustard might protect against leukemia, where there are too many leukocytes. This led to the first chemotherapeutic agent and the founding of the Sloan-Kettering Institute for Cancer Research. It also marked the beginning of oncology's war on DNA.

Until the recent advent of CAR-T cells, the goal of chemotherapy has been to kill cells undergoing replication. Nitrogen mustard (bis(2-Chloroethyl)methylamine) is an alkylating agent that reacts with DNA. Other chemotherapeutic agents, such as cyclophosphamide (another alkylating agent), metho­trexate (an antifolate), etoposide (a topoisomerase inhibitor), vincristine (a mitosis inhibitor), imatinib (a protein kinase inhibitor), all have one thing in common: they kill cells when they're trying to divide.

This explains the hair loss and gastrointestinal side effects of cancer treatment, because hair follicle cells and cells in the small intestine grow rapidly. But these cells will grow back once the chemo stops. Neurons aren't so lucky: neurons in the brain cannot be replaced (though some neurogenesis can occur in the dentate gyrus, a region of the hippocampus, it's not nearly enough). Luckily for neurologists, most of these chemotherapeutic agents cannot cross the blood-brain barrier. Even though neurons in the brain are post-mitotic, they can be damaged or killed by chemotherapy. This would cause dementia.

Are Cancer and Alzheimer's disease opposites?

It's now clear that the observation that patients with cancer are less likely to die from Alzheimer's disease is not just an artifact of death certificates, but a real phenomenon.

A 2018 paper in Nature (discussed here) illustrates what's going on. The authors discovered that gene fragmentation and recombination were occurring in Alzheimer's disease brain, which is to say somatic mutations were occurring (somatic mutations are mutations that don't happen in germ cells and so aren't passed on to your children). This was an important discovery, so, naturally, the authors ignored it and focused on the fact that some of the mutations were occurring in amyloid precursor protein and presenilin-1 and 2, which are the villains in the "bad protein" theory in Alzheimer research that is dominant even today.

What their paper really showed was that something was breaking down the DNA in Alzheimer patients. Hydrogen peroxide is good at doing this, and we know that peroxide is increased in AD patients. So is gamma radiation, which reacts with water to produce hydroxyl radicals, which are even worse for DNA than peroxide. This, of course, is why oncologists use it.

Maybe you might say advocating for a "bad small molecule" theory is just as short-sighted. After all, hydrogen sulfide, cyanide, and nitric oxide are toxic small molecules, but they're essential for life.

DNA Repair

The war on DNA has led to an explosion of knowledge about DNA repair. It's been estimated that every cell in your body gets between 10,000 and 100,000 DNA breaks every day caused by oxidized molecules known as ROS, reactive oxygen species, which include hydrogen peroxide, superoxide, and hydroxyl radicals.

Oncogenes like MYC and mutated forms of RAS protein cause cells to enter into the S-phase of mitosis before the DNA is ready, causing it to break. This activates the DNA Damage Response, a complex set of enzymes that detect the broken DNA and repair it. This is called replication stress, and there are two main enzymes involved in DNA repair: ATR and ATM.

Simple repairs like cross-linked bases, caused by alkylating mutagens Part of the repair process is the creation of a replication fork, where the good DNA is getting fixed by comparing the two strands. Sometimes the replication fork stalls, sometimes because deoxynucleotides get depleted, or a "lesion" in the DNA causes the repair to screech to a halt. This can cause the second strand to break as well, and it's a disaster for the cell: single-stranded DNA is exposed--a very bad thing, as ssDNA rapidly gets chewed up. A protein called MMR detects the damage and orchestrates a whole series of repair proteins: RPA to shield the ssDNA, ATR, and ATM is called in.

The cell has several ways of repairing double-stranded DNA breaks: Homologous Recombination Repair (HRR), Non-homologous end-joining (NHEJ), Alternative non-homologous end-joining (Alt-NHEJ), and Single-strand annealing.

One of the most important receptors in the immune system is TLR4, one of many toll-like receptors in the body. TLR4 classically reacts to many things, including lipopolysaccharide or LPS. LPS is produced by bacteria and forms part of its outer cell wall. It may surprise you to learn that cancer researchers regard LPS as a cause of cancer metastasis.

To understand why, we need to understand some immunology.

A crash course in immunology

Humans have two different immune systems: the innate immune system, and the adaptive immune system. In the innate immune system, specific proteins on the cell surface act as "pattern recognition receptors". When a pattern, which is to say a specific type or shape of molecule, is detected, the cells release cytokines and chemokines, which are small proteins that initiate a complement response that culminates in other cells called macrophages that engulf, puncture, and kill the invading pathogen.

It is called the innate system because it's always present. It doesn't use antibodies and it has no need for prior exposure to an antigen. The receptors have fixed responses to things that signify the presence of a pathogen, like single-stranded DNA, lipopolysaccharides (which are made by bacteria), and other things that shouldn't be there.

When they detect something, they release cytokines and chemokines that activate the complement system. The complement system is much like the blood coagulation system: it is a cascade of proteins in a that proteolyze other proteins in a specific sequence, breaking them down into smaller proteins. This provides security, as it's essential to keep the complement system from being triggered accidentally, and it also allows a small signal to be amplified to produce a massive response.

At the end of a long and complicated sequence of events, the complement proteins assemble into a complex that punches holes is the invading cells, killing them. Macrophages then smell the mess and come along to clean it up by engulfing it and digesting it.

We're all familiar with this response: the innate system is the one that gives you a fever, runny nose, and pain when it's activated. These symptoms of infection aren't caused by the pathogen, but by the innate immune system's response to it, which is why some doctors worry that antipyretics, which block fever, might be prolonging the infection by interfering with our response to it.

Adaptive immune system

Below is an oversimplified crash course on the adaptive immune system.

Only higher animals have an adaptive immune system. Your adaptive immune system consists mainly of three types of cells:

1. B cells, which produce antibodies and cytokines. The antibodies bind to pathogens that are floating around in the bloodstream or accessible on the surface of other cells. B cells can't detect pathogens that are inside infected cells.
2. Dendritic cells, which float around checking for infected cells. Like tiny rat finks, the dendritic cells report what they've found to the T cells.
3. T cells, which attack the body's cells that are infected, which is to say cells in which the pathogen is hidden inside. The T cells can find these cells thanks to the MHC/HLA system, which takes bits and pieces of whatever proteins are inside the cell and puts them on the surface, ‘presenting’ them to the immune cells. If the T cells find something they don't like, they kill the cell. This is obviously risky, so it's tightly regulated. When it goes wrong we get an autoimmune disorder.

When the T and B cells discover a new antigen, the cells do an almost magical thing: they evolve. Nature uses a form of deliberately accelerated evolution by shuffling their DNA by a process called V(D)J recombination and then randomly mutating the antibody DNA by a process called somatic hypermutation. A process of selection, similar to the Darwinian natural selection among animal species, then selects for those cells that produce the best antibody. Those that are most effective survive; the rest get a second chance to evolve. If they fail a second time, as almost all of them do, they die. This is a time-consuming process and our other immune system, called the innate immune system, tries to attack the pathogen first. But it is not nearly as powerful.

june 26 2021, 6:24 am