I carry my son's DNA: a look at microchimerism and its effects

To celebrate the upcoming release of my detective thriller CHIMERAS, the next few Research Blogging posts will be dedicated to the different forms of chimerism. I'm sure you are all familiar with dispermic chimeras, which occur when two fertilized eggs fuse together shortly after conception. The result is one individual with two sets of genetically distinct cells.

Have you ever heard of microchimerism, though?

"Microchimerism refers to a small number of cells (or DNA) harbored by one individual that originated in a genetically different individual. While microchimerism can be the result of interventions such as transplantation or transfusion, by far the most common source is naturally acquired microchimerism from maternal-fetal trafficking during pregnancy [1]."

Before the 1960s, it was believed that the placenta was a perfect barrier between mother and fetus, and no blood or cells could trespass it in either direction. Today we know that there's actually a two-way exchange of cells between mother and fetus during pregnancy. What's even more surprising is that these "extraneous" cells outlast the duration of the pregnancy and can in fact be found in the child and/or the mother years after birth. Male DNA has been found in women years after they had given birth to their sons. In fact, fetal cells are released in high quantities during spontaneous abortions, hence can be found even in women who have never delivered, so long as at some point in their lives they became pregnant.

This of course prompts the following question: is microchimerism beneficial to the mother's and/or child's health?

The answer is yes and no.

For example, things can go wrong when the mother develops some kind of malignancy during pregnancy: there have been cases in which metastases from a maternal melanoma were acquired by the baby through transplacental transfer. Conversely, it has been noted that the amount of fetal DNA circulating in the mother is higher in cases where there are anomalies in the fetus's chromosome count and in pregnancies complicated by eclampsia (seizures).

Where is the fetal DNA found? Just about everywhere: liver, thyroid, cervix, gallbladder, intestine, spleen, lymph nodes, heart, and kidneys. Once they enter the maternal system, the fetal cells act effectively as an engrafting, and that's how in some cases they can persist for years.

Some studies indicated that the HLA type of the fetal cells (HLA is the most variable family of genes in our genome because they encode an important part of the immune system; these genes are responsible for our ability to recognize different pathogens) circulating in the mother may affect the mother's risk of later developing auto-immune disorders, systemic sclerosis in particular.

There are beneficial effects, too:

"As previously noted, fetal cells that appear to have differentiated into organ-specific phenotypes have been found in some patients with thyroid or liver damage, suggesting a role for fetal microchimerism in repair (Srivatsa et al. 2001; Stevens et al. 2004) [1]."

In other words, these fetal cells could have been recruited to the damaged tissue in an attempt to repair the lesions.

What about the effects of maternal cells circulating in the fetus?

"Fetal acquisition of maternal cells may have even more dramatic consequences on later fetal health than fetomaternal transfer does on maternal health [1]."

Maternal cells have been found in numerous fetal tissues: fetal liver, lung, heart, thymus, spleen, adrenal, kidney, pancreas, brain, and gonads. Maternal cells are able to migrate to an organ and differentiate into a local phenotype -- something that is truly intriguing, as the mechanism by which this happens could help inform organ regeneration research. Numerous autoimmune disorders like neonatal lupus, for example, have been associated with high levels of maternal microchimerism. However, it's not clear if the higher concentrations have a pathogenic effect and therefore cause the disease or, instead, are an effect of the disease. It could be that, for example, the maternal cells are recruited in higher concentration in an attempt to repair the damaged tissues. For example, one of the studies discussed in [1] found a beneficial role of maternal microchimeric cells in type I diabetic pancreas.

[1] Gammill HS, & Nelson JL (2010). Naturally acquired microchimerism. The International journal of developmental biology, 54 (2-3), 531-43 PMID: 19924635

CHIMERAS, detective thriller meets science

We all have it and yet we no longer use it: ancestral DNA, the genetic footprints left by our ancestors. Base after base of pseudogenes, genes that once made us predators and hunters, that controlled our sense of smell, our instincts, our impulses. Genes that today are completely silenced.

What if ... one day ... in one person ... those genes suddenly awakened ?

"Haunted by the girl he couldn't save in his youth, and the murder he committed to avenge her, Detective Track Presius has a unique gift: the vision and sense of smell of a predator. When a series of apparently unrelated murders reel him into the depths of genetic research, Track feels more than a call to duty. Children are dying, children who, like himself, could have been healthy, and yet something, at some point, went terribly wrong. For Track, saving the innocent becomes a quest for redemption. The only way he can come to terms with his dark past is to understand his true nature."

So here's the deal: CHIMERAS is coming out soon. It's a matter of weeks now. No, I'm not looking to get famous or hit the New York Times bestselling list. To be honest with you I love my comfort zone, which is exactly where I'm at right now. But. I had an idea. Four years ago. And the idea was, and still is, unique. Vampires have been done. Ghosts have been done. Spaceships, apocalypses, dystopian, genetically modified humans, genetically enhanced humans, genetic monsters, super-viruses, drugs, smuggling, prostitutions, serial killers -- I read them all and loved them all. But they all have been done before.

Epigenetics has not been done. Not in fiction.
That's all I want, really. I want my idea out.

I had quite a roller coster, between agents' offers (8!), publishers' rejections, publishers' requests for changes, etc, etc, etc. One day I'll tell the whole story. Maybe I'll write a book on that -- haha, that would be quite ironic. But all I want for now is my book out.

And here's where you come into play: do you love science and scientific mysteries? Do you enjoy books and thrillers in particular? Then be the first one to review CHIMERAS! For a limited time only, I'm offering free Kindle copies of CHIMERAS. Send me an email at eegiorgi(at)gmail.com with the subject line "ARC copy" to get a free Kindle copy of my book. This copy will be for your personal use only. By signing up you agree to write an honest (yes, honest: I'm not looking for 5-star reviews, I'm looking for what you honestly thought of the book) and post it either on Amazon or Goodreads (preferably both).

Please, support me in my new adventure: tell your friends and share this post! You can read the prologue here and share that post, too. Please don't share the book copies themselves, as I'd like to keep track of exactly how many copies I'm sending out to the world. So, if you know anybody who might be interested, tell them to write directly to me. Again: eegiorgi(at)gmail.com, subject line "ARC copy".

Follow the blog and subscribe to the post to make sure you don't miss the release date! And cheer me on because I'm terrified so excited I think I'm going to pass out. :-)

Transcription factories for gene expression: the hard working units of the nucleus

You've probably heard it many times already: if you could stretch out the DNA contained in any one nucleated cell in your body, it would be 2 meters (~6 feet) long. Now imagine packing this 2-meter long molecule into a sphere whose diameter is of the order of a few micrometers, roughly one millionth smaller than a meter. Yes, it's going to be packed in there, yet those genes have to be accessible to the "workers" that come in and perform daily tasks such as gene transcription, replication, and DNA repair. Clearly, which genes are accessible and which aren't is going to play a major role in the cell's life and development.

The chromatin, the ensemble of DNA and proteins inside the nucleus, is dynamically regulated. For gene expression, active genes relocate from chromosome regions and cluster into subnuclear compartments called "transcription factories for gene expression."

As you know, transcription is one of the fundamental steps in the making of proteins: the enzyme RNA polymerase II creates a complementary strand of RNA (a precursor of mRNA) from the active gene. The mRNA is then synthesized and translated into the protein's amino acid sequence. The concept of transcription factories comes from the observation that specific regions in the nucleus are highly enriched in RNA polymerase II, and those are the regions from which new RNA transcripts emerge. A second observation is that distant loci, often on different chromosomes, can interact during regulation through long-range regulatory contacts.

"Increasing numbers of examples suggest that regulatory DNA elements also seem capable of undergoing functional contacts with genes located on other chromosomes. [...] By contrast, temporarily inactive alleles are positioned away from transcription factories, suggesting that genes migrate to these subnuclear sites in order to be transcribed. Crucially, the number of transcription factories per cell is severely limited compared to the number of expressed genes, compelling genes to share the same transcription factory [1]."

The above figure is a schematic of a transcription factory: active genes from different chromosomes are recruited from the chromatin. As transcription proceeds and new RNAs are formed, the templates are reeled through the factory bringing downstream nearby genes. Transcripts generated in a transcription factory that are in close proximity have a greater chance to undergo trans-splicing, in other words, the two transcripts are joined into one even though they originated from different RNA polymerases. The resulting joint RNA is called chimeric RNA. A few studies have observed proteins generated from chimeric RNAs.

In addition to trans-splicing, close proximity in a transcription factory increases the chances of translocation, i.e. one genomic region being moved to a different locus.

"It is puzzling that a genome conformation that increases the risk of potentially grave translocations can evolutionarily persist. We speculate that three- dimensional gene clustering of transcribed loci must elicit evolutionary advantages that outweigh the dangers of translocations."

As Schoenfelder et al. conclude,

"A major challenge will be to decipher the relation between these genome conformation changes and the numerous epigenetic alterations of the genome, allowing their integration into a comprehensive picture of the spatial and functional organization of the nucleus."

[1] Schoenfelder, Stefan, et al. (2010). The transcriptional interactome: gene expression in 3D. Current Opinion in Genetics DOI: 10.1016/j.gde.2010.02.002

A chimeric virus to cure leukemia? Yes, we can!

Last week I talked about gene therapy and vaccines targeting tumor cells. Following those posts, a friend of mine (thanks, Alex!) pointed me to a recent case report published in the New England Journal of Medicine, which describes a successful use of gene therapy to treat leukemia [1]. Since you know I like to talk about chimeric viruses and all the wonderful things you can do with them, I was instantly drawn to the paper.

Leukemia is a type of cancer that causes an abnormal increase in white blood cells. The patient discussed in the NEJM case report was affected by a type of leukemia called B-cell neoplasm, which, as the name indicates, causes the abnormal proliferation of B-cells.

So, how do you address the problem using gene therapy?

This is what we need: (a) a target on the tumor cells that will tell the immune system to destroy them; (b) a weapon for the immune system to recognize and kill the tumor cells; (c) a way to "give" the weapon to the immune system.

The answer to (a) comes from a receptor called CD19, which is expressed by malignant B-cells. The "weapon" (b) is a genetically engineered anti-CD19 antigen receptor, which enables T-cells (our immune system "soldiers") to recognize the malignant B-cells and destroy it. The big question is (c): how do we make T-cells with the anti-CD19 antigen receptor?

This is where gene therapy and chimeric viruses come into play. How do we use gene therapy to transfer the genes that express the anti CD19 antigen receptor into the T-cells? We need "something" that does this for a living -- transfer genes into cells. Remember what that is?

Absolutely, a virus.

Now, remember what virus in particular targets T-cells?

HIV, of course!

And that's exactly what the authors of this study did: they created an HIV chimeric virus and endowed it with the genes of the anti-CD19 antigen receptor. T-cells were collected from the patient, transduced (which means that the genetic material was transferred inside the T-cells using the modified HIV virus), then infused back into the patient.

Like in all best stories, at first things seemed to go terribly wrong: two weeks after the transfusion, the patient started having high fevers; three weeks after treatment the patient had to be hospitalized and treated for metabolic complications consistent with leukemia treatment.

And then the miracle. One month after the infusion there were no more tumor cells in the patient's blood. At the time the paper was written -- ten months after the therapy -- the patient was still in remission, and the antigen recognizing T-cells were still proliferating.

Interestingly, this case report reminds of an almost symmetric case reported in 2008: an HIV-positive patient who developed leukemia was treated with a bone marrow transplant from a donor who had the Delta32 CCR5 mutation I discussed in this post. The mutation modifies T-cells in a way that they can no longer be infected by the HIV virus and, indeed, after the bone marrow transplant, the patient's viral load dropped and never recovered. As far as I know, the patient is the only one ever to be cured of AIDS.

[1] Porter, D., Levine, B., Kalos, M., Bagg, A., & June, C. (2011). Chimeric Antigen Receptor–Modified T Cells in Chronic Lymphoid Leukemia New England Journal of Medicine, 365 (8), 725-733 DOI: 10.1056/NEJMoa1103849

How did that pesky virus end up in our DNA?

Last time we talked about the different types of genetic and epigenetic chimeras. We learned what a chimeric virus is, and that retroviruses need to get integrated into the host's DNA in order to replicate. They basically inject their RNA into the cell, the RNA gets transformed into DNA, the viral DNA enters the cell's nucleus and once in the the nucleus it's integrated into the cell's DNA.

This process has been going on for as long as viruses have existed. And viruses have existed for a long time.

Normally we think of viruses as pesky little things. Flu viruses are annoying, more serious viruses like HIV or HCV are deadly. Well, you'll be surprised to know that over the course of evolution, viruses have driven genetic diversity by transferring genes across species. How do we know that? We know because we all carry ancestral DNA derived from viruses in our genome. There are roughly 100,000 copies of endogenous retroviral DNA in our genome [1]. In other words, we're all chimeras!

But... how did the retroviral DNA get there?

The mechanism is fascinating. You see, when a virus enters the body, it has one purpose: replicate, and to do so it needs to infect cells. Every virus has its own preferential cells. HIV, for example, infects mostly T-lymphocytes, but it also creates huge reservoirs in the guts. So imagine a platoon of viral particles trying to eat up whatever they can as they migrate around the body. Well, sooner or later, some virus will find a very special set of cells: the gametocytes, a.k.a. oocytes in women, and spermatocytes in men. And once in there the virus is stuck. Because you see, gametocytes will not duplicate unless they get fertilized. But by then the virus is no longer active. It's literally stuck, in the sense that the integrated viral DNA now cannot replicate and cannot escape the host's DNA.

What happens if the infected gametocyte gets fertilized?

Once fertilized, the cells start reproducing very fast. Every cell in the newly created embryo will carry the bit of viral DNA, which has now become non-coding. The new individual will carry the viral proteins everywhere, even in his/her own gametocytes, and hence the viral proteins will be inherited by his/her offsprings as well.

And that's how viruses ended up in our genome a long, long time ago.

Wait, my story isn't over yet. Now I'd like to convince you that this hasn't been some futile genetic exercise. Remember, I'm a fan of non-coding DNA. It holds the key to evolution. And as species continued to evolve, sure enough, Mother Nature found a way to use those non-coding viral proteins. The viral genes became beneficial to the host. 

Here's the scoop: viral genes are expressed in the placenta [2]. Why? Well, we don't know for sure, but the hypothesis are intriguing [3].

Retroviruses debilitate the immune system. In general, this is not a good thing for the body, except in one very special instance: an embryo is literally a parasite growing inside the mother's body. It carries extraneous DNA and, under normal circumstances, something carrying extraneous DNA would be considered by the immune system an antigen. But a fetus is not to be considered an antigen. Therefore, the expressed viral proteins found in the trophoblasts, the outer layer of the placenta, would have the role of suppressing a possible immune reaction against fetal blood.

Another property viruses have is that of cell fusion: they literally "merge" cells together into one membrane. A second hypothesis is that this property is used during the development of the placenta to build a barrier between the maternal circulation and the fetal circulation.

Let me conclude with a caveat: as always, when talking about evolution, it's easy to slip into thinking that certain genes evolved to fulfill a specific function. In reality, we know the placenta evolved because it presented an advantage compared to laying eggs. The beauty of DNA is that it holds not just the present information, but the memory of the information needed to get there. It's this redundancy that allows it to explore new solutions, but it's only a posteriori that we can retrace this path and give it a meaning.

REFERENCES:
[1] Emerman M, & Malik HS (2010). Paleovirology--modern consequences of ancient viruses. PLoS biology, 8 (2) PMID: 20161719
[2] Dunlap KA, Palmarini M, Varela M, Burghardt RC, Hayashi K, Farmer JL, & Spencer TE (2006). Endogenous retroviruses regulate periimplantation placental growth and differentiation. Proceedings of the National Academy of Sciences of the United States of America, 103 (39), 14390-5 PMID: 16980413
[3] Dupressoir A, & Heidmann T (2011). [Syncytins - retroviral envelope genes captured for the benefit of placental development]. Medecine sciences : M/S, 27 (2), 163-9 PMID: 21382324

Picture: Onion blossom. Canon 40D, shutter speed 1/500, focal length 85mm. The deer repellent spray may have something to do with the weird horn-like growth. It's been three months and the thing hasn't blossomed yet. I think next time I'll let nature take its course.

Chimeras unveiled: genetics versus epigenetics

You think you know everything about chimeras? Well, think again: today I'm about to surprise you.

Let's start from the very beginning: in Greek mythology the Chimera was a monster, part goat, part snake and part lion.

Like with many other things, genetics borrowed the term to define organisms that are the result of genetically different tissues fused together. This happens at conception, when two fertilized eggs fuse together to form a single individual. Conceptually, it's the exact opposite of identical twins, where one fertilized egg splits into two identical individuals. Chimeric animals, for example, will present bits of fur of different colors. A chimeric person may show different pigmentation across his or her body. The individual will have two distinct DNAs in different tissues.

I'm sure so far I haven't told you anything new.

One day one of our experimentalist collaborators called to tell us they'd found a chimera. He was quite excited about the discovery. I scratched my head. Because you see, he was talking about HIV. And the thing with HIV is that it has one molecule of RNA. Just one, that's all there is. And so, how can a virus be the result of "tissues" coming from different genomes?

It turns out the definition is slightly different for viruses. A chimeric virus is a virus that has bits of extraneous DNA in its genome. Here I should be careful: HIV is a retrovirus, which means a free viral particle carries RNA, not DNA; however, once it enters the cell, an enzyme called reverse transcriptase turns it into DNA and, as DNA, it enters the host cell's nucleus and gets integrated into the host's DNA. This integration is what allows the virus to replicate. It's also what caused our chimeric virus to integrate in its own genome part of the host's genome.

The concept is used in gene therapy: a retrovirus is basically a shell (called envelope) with genetic material inside, and it's designed to inject the genetic material into the cell's nucleus. This is a fundamental step in the retrovirus's life because without it, it can't replicate. Many gene therapy clinical trials have exploited this mechanism by genetically engineering a chimeric retrovirus that carries human genes. Once the virus enters the nucleus, it delivers the new genes, thus "fixing" the problematic ones. I will talk more about gene therapy in a future post.

So now you've met a new type of chimera. Wait, it's not over yet.

Remember when I introduced the concept of epigenetics? Remember what pseudogenes are? They are ancestral or redundant parts of our DNA that are usually non-coding. We learned in those earlier posts that epigenetic processes do change during one's lifetime, and, as a result, pseudogenes can be activated and become coding genes. They are called chimeric genes.

An individual with chimeric genes is what I call an epigenetic chimera. The individual has the same DNA across all of his or her tissues, but some cells express genes that are otherwise non-expressed in the species.

In summary, we have three types of genetic chimeras: individuals with different DNAs; viral particles integrating different bits of extraneous DNA; and individuals expressing different chimeric genes.

Now that you know the different types of genetic chimeras, you are ready to learn why you and I are chimeras, too. 

Picture: Statue of Hutshepsut, Metropolitan Museum of Art, New York City. Canon 40D, focal length 85mm, shutter speed 1/10. Hutshepsut was a female pharaoh, often depicted in a masculine attire and with the typical pharaoh beard, symbol of pharaonic power.