Stem Cells to Treat Spinal Cord Injury

Journal Club: Intravenous multipotent adult progenitor cell treatment decreases inflammation leading to functional recovery following spinal cord injury

Written by DePaul, et al. in the journal Scientific Reports. The complete article is here.

Background: Stem cells are unique in that they can divide indefinitely and can turn into multiple different types of cells (see image below).  For example, during human development, embryonic stem cells have the ability to turn into all of the different cell types throughout the body – such as liver cells, lung cells, and skin cells. Embryonic stem cells are called pluripotent stem cells for this reason.  Stem cells have also been found in adults, but they are usually able to turn into only one or several types of cells (called multipotent stem cells).  Scientists have thought that this ability for stem cells to continually grow and turn into different cell types could be harnessed to treat a number of diseases that involve cell death, including spinal cord injury.

Stem cells - wikipedia

By OpenStax College [CC BY 3.0], via Wikimedia Commons


The authors of this paper are interested spinal cord injury (SCI).  When the spinal cord (the bundle of nerves that goes down your back) is injured when something disrupts the vertebrae (like it being hit during a car accident) this can tear or push on the spinal cord.  This causes damage to the nerves and prevents electrical signals between the body and the brain from being transmitted properly, often resulting in paralysis. The authors were interested in studying whether stem cells could help reverse the damage that’s caused by this type of injury.

Results: In this publication, the authors isolate stem cells called multipotent adult progenitor cells (MAPCs) from the bone marrow. To break this down, “multipotent” means that the stem cells can turn into several different cell types. “Progenitor” cells are actually more specified than stem cells – stem cells can divide forever, but progenitor cells can only divide a certain number of times. “Adult” means that these cells are taken from the adult bone marrow.

Because you can’t just inject cells into humans with spinal cord injury (that would have to be a clinical trial WAY down the road once there is evidence that it works in animals), the authors use a “model” of spinal cord injury in rats. Technically – they crush the rat’s spine (eek).  In case you’re interested, here’s the device they use to do this. The rat then has decreased mobility and inability to urinate on it’s own – like what might happen in the case of a paralyzed person with a spinal cord injury.

The researchers injected multipotent adult progenitor cells into the rat after injury to see if they reverse these mobility and urination effects.  Interestingly, when MAPCs are injected into a rat vein the day of injury, nothing happened. However, if the MAPCs are injected 1 day after injury, the rats recover some mobility and the ability to urinate on their own compared to rats without treatment.

One might assume that the MAPCs do this by going to the injured area of the spinal cord and re-growing nerve cells.  However, the authors found that this wasn’t the case.  In fact, the MAPCs moved to the outside edges of the injury and even more to the spleen (see image below).  The spleen is where many of the body’s immune cells are stored. In spinal cord injury, the immune system is a double-edged sword.  The immune system cleans up the damage from the injury itself but also attacks the injury and makes more damage.  There is evidence from this paper that the MAPCs in the spleen decrease the damaging effect on the spinal cord injury from the immune cells in the spleen.

figure 6 SCI

Figure 6 from the paper. The green dots are labeled multipotent adult progenitor cells (MAPCs). They are labeled green so that you can see where they are located in the rat’s body.

Conclusion: This paper presents a promising result that provides hope for this type of therapy in spinal cord injury patients.

Sci Snippet: Cancer vs. Tumor: What’s the difference?

It doesn’t matter to you what word you hear if you or a loved one is told by a doctor, “You have cancer” versus “You have a tumor.” Either way, there’s a wave of fear that is likely sustained through months, years, or a lifetime of treatment. It’s a diagnosis that nearly everyone has been touched by, so it’s something that everyone has talked about at one time or another.  The words tumor and cancer are typically used interchangeably, especially by people who are not in healthcare.  But it helps to know that there is an important distinction between cancer and a tumor when describing a mass of cells growing somewhere in the body.

The most important point is that a tumor DOES NOT mean cancer.  A tumor is a whole bunch of cells growing out of control (think of it as the cell turning on the gas pedal for cell division) creating a mass somewhere in the body.  Cancer, on the other hand, means that these cells have the potential to move and invade other parts of the body.A tumor can be benign (not cancer) or malignant (cancer).

Image of a benign meningioma. Thanks to Wikipedia for the image.

Image of a benign meningioma. Thanks to Wikipedia for the image.

What does it mean to be benign? A benign tumor still a huge mass of cells, and even though it may not spread to other parts of the body (the definition of malignancy and cancer), the mass could grow so large it presses against vital organs requiring surgical removal or causing death.  An example of a benign tumor is a meningioma.  This is a brain tumor that grows out of the covering of the brain and spinal cord, called the meninges, and although they do not typically spread to other places in the body (so they are not considered cancer), they do put pressure on the brain and spinal cord and usually have to be removed and may be treated with radiation.

benign_malignant

Thanks MedicineNet.com for the image

Cancer, on the other hand, is a tumor that has the potential to spread to other parts of the body, which is called malignancy.  This is one of the reasons that cancer is called cancer – from the Greek meaning crab because of the crab-leg like projections that are found in tumors that are invading neighboring tissue.  Tumors may be benign, malignant, or transition from something benign to something malignant.  For example, in the breast, masses of cells can form like papillomas that are a benign tumor that will not spread to other areas of the body. However, a breast cancer diagnosis implies that the breast tumor has the possibility to spread.  The only way to know whether a lump is a papilloma, breast cancer or something else is through a doctor and a biopsy.

It’s also important to note that not all cancers involve a tumor.  A great example of this are blood cancers that involve the increased growth of a particular type of blood cells, but will not have a tumor.

And in case you’re wondering where cysts fit into this, these are sacks filled with fluid, air or some semi-solid material. Cysts can be caused by a number of things including infection or clogging of glands. They may indicate a risk factor for a tumor or cancer, but are not cancerous themselves.

 

How not to die when working in the lab – Biosafety

What’s your biggest concern for your safety when walking into work each morning? That you’ll get a papercut or burn your tongue on your morning coffee? Maybe if you’re in a higher risk profession (like a contractor) you’re worried about something falling on your head.  As a scientist, may researcher enter the lab every day and have to worry about being infected by what they are researching!

blood tubes

Blood tubes collected for our biobank

Human tissue and blood may contain viruses like HIV or hepatitis that’s just needs entry into your body through a cut or in the mucus membranes of your nose. Or maybe you’re working with viruses like the flu to see how they infect cells. And what of those people who are studying the deadliest diseases like Ebola – how do they study these diseases or work to develop vaccines or treatment drugs without getting Ebola themselves? BIOSAFETY!

Wow. Boring. Right? Well, kind of. I spent this last week taking a refresher course on biosafety and the reading was DULL, but sitting down to think about all of the implications it becomes fascinating.

The thing is, anything that would infect you is likely invisible.  If you’re working with human tissue or blood, you can see the blood but not what might be inside of it (bacteria or a virus) that could infect you.  And if you drop a blood tube on the floor, you can see the pool of blood but not the microscopic aerosolized droplets in the air just waiting to be inhaled. So how does a scientist take care of these hazards not just so they don’t get sick but so they don’t infect the public as well?

Good news is that scientists think about this a lot.  First, depending on what you’re working on depends on how careful you have to be. Compare this to the difference between giving a 4-year-old plastic play-doh scissors versus sharp surgical scissors – they have different risks associated with them and you’d treat the kid using them in different ways.  In the same way, working with things that are not known to infect humans and cause disease (like bacterial cells) don’t need to be handled as carefully as those that cause deadly diseases that are spread through the air (like Ebola).  This is what defines the “risk group” on a scale of 1-4, where 1 is the lowest risk and 4 is the highest. The play doh scissors or bacterial cells would be Risk Group 1 and the sharp surgical scissor or Ebola virus would be Risk Group 4.

This then helps researchers figure out what protective measures need to be taken – also called Biosafety Levels (abbreviated as BSL) 1-4.  For example, level 1 can be done in the laboratory out in the open wearing a lab coat and gloves.  Level 2 requires research to be done in a biosafety cabinet so that anything that spills or is aerosolized is contained.  Level 3 is for agents that cause moderate to severe disease and in this case the experiment needs to be completely contained in a glove box or in a special room with controlled air flow. Level 4 is for agents that cause lethal disease that has no treatment or cure (like Ebola). In this case the BSL-4 is what you may see on TV or movies where researchers are fully enclosed in a “space suit” to prevent any contact between the person and the agent.

biosafety

In my lab, we regularly work with human tissue and blood and because the tissue or blood may be infected with certain biological agents, they are considered risk group 2. We always wear a lab coat and gloves and work inside a hood.  When moving these tubes from one place to another, we make sure that there are at least two layers of containment – the blood tube is the first layer and this is inside a plastic bag as the second layer. We also get re-trained every year to make sure we remember how to handle spills (just in case).

Now because we’re all morbid creatures, I’m sure you’re wondering what’s happened when this hasn’t worked. Here is an article about the most common infections acquired in the lab and how they were acquired.  For more newsy stories, here is a story about a researcher who contracted plague in the lab. Eek! Definitely reinforces the importance of being careful in the lab.

Journal Club – A mutation in mice to study ALS

Amyotrophic Lateral Sclerosis (ALS) is a debilitating neurodegenerative disease that affects neurons in the brain, brain stem, and spinal cord. When these neurons die, it affects the connections that they have to muscles throughout the body resulting in muscle weakness that affects speaking, swallowing and breathing leading to paralysis and eventual dead.  The cause of ALS isn’t known in 90-95% of cases.  However, recently scientists have identified a mutation in a gene nondescriptly called “chromosome 9 open reading frame 72,” which is abbreviated to C9ORF72.  This mutation results in six nucleotides, GGGGCC, being repeating up to 1000 times within this gene in ALS patients.  Even though this is the most common mutation found in ALS patients, it’s still unclear exactly how these repeats affect neurons or the progression of the disease. The two hypotheses that are most studied are that the mutated C9ORF72 makes mutated RNA transcripts (RNA is the molecule that usually helps DNA be translated into proteins) or makes unusual proteins called dipeptide repeat proteins (DRPs), each of which can aggregate (clump) together and disrupt the normal activity of the neurons leading to neurodegeneration.

neuron_als_c9ORF72

The pink dots show clumped up RNA from the many many repeats in the C9ORF72 gene. Each panel shows these clumps in different areas of the mouse brain. Taken from the article Peters et al. 2015 Neuron

In two recent publications in the journal Neuron, researchers have used mice as a model system to look at how these large GGGGCC repeats in C9ORF72 affect the mouse nervous system.  Why use a mouse? First, scientists know how to experimentally change the mouse genome in order to add hundreds or thousands of repeats to a single gene, like C9ORF72.  Second, mouse and human genes are about 85% identical, so if scientists can understand how a gene like the mutated C9ORF72 affects neurons in mice, it may also help scientists understand how it works in humans. Third, by creating a mouse “model” of ALS, scientists can use this model to better understand ALS and to test potential future therapies (it’s worth noting that only one drug currently exists for ALS and it typically extends life only by a few months).

In each article, the mouse model was slightly different – one had a mutated C9ORF72 with 500 GGGGCC repeats and the other varied between 100-1000 repeats. However, both sets of researchers found the same results.  The mice had aggregated RNA transcripts and DRPs in their neurons just like what are found in human patients with ALS, but none of the mice had behavioral changes or neurodegeneration that are seen in human ALS patients.  So why didn’t the clumped up RNA and proteins cause neurodegeneration in mice like they do in humans?  There are lots of potential reasons – including the fact that even though mice and humans are similar, there are still lots of differences and mice may respond to these aggregated RNA and proteins differently than humans.  However, the authors of these papers suggest that other environmental and/or genetic factors along with the aggregates caused by the C9ORF72 mutation must be involved in developing the neurodegeneration.  It may also mean that getting rid of these aggregates before neurodegeneration occurs may prevent development of ALS.  Now that these mice are available to study, they should help in identifying the other factors involved in ALS development along with developing possible treatments for this debilitating disease.

Want to read the articles?  Unfortunately, they are behind a paywall, but you can see the abstracts here:

O’Rourke et al. (2015) C9orf72 BAC Transgenic Mice Display Typical Pathologic Features of ALS/FTD. Neuron. Volume 88, Issue 5, p892–901, 2 December 2015 Article

Peters et al. (2015) Human C9OFR72 Hexanucleotide Expansion Reproduces RNA Foci and Dipeptide Repeat Proteins but Not Neurodegeneration in BAC Transgenic Mice. Neuron. Volume 88, Issue 5, p902–909, 2 December 2015 Article

Read the Article from PN News that I contributed to here

Institutional Review Board (IRB) – Keeping Research Subjects Safe

Xmas

I was working over the holiday weekend, but at least I was working in my decorated living room with a fire going (the high in Arizona was only 66 today!!)

Hope you had a fabulous Thanksgiving weekend! Four day weekends are great, and even I took some time off to enjoy the holiday with my husband and the puppies.  And then I got back to work because I have an Institutional Review Board (shortened usually to the acronym IRB) meeting in two weeks and the committee has eight new protocols to review. This likely means very little to you, but the IRB is what ensures that the rights and welfare of humans participating as subjects in a research study are adequately protected. And here’s why that’s important…

In a previous post, I explained clinical research.  Clinical research studies new drugs or devices to determine if they are safe or effective. As you can imagine, at a world-class hospital, we have hundreds of clinical trials. You can check out information about these clinical trials by following the links for the Barrow Neurological Institute, St Joseph’s Hospital and Medical Center and the University of Arizona Cancer Center at Dignity Health.  Physicians and surgeons are studying new treatments for many different cancers, devices like the NovoTFF for glioblastoma, and comparing new drugs or combinations of drugs to current treatments to see if the new regime works better.

Now if a  company wants to test a new drug, they can’t just pick up the phone and ask their physician buddy if they could just use a few of their patients to test some stuff out. But why not?  Honestly, it’s because at one point researchers did some pretty crappy things in the name of science.  Thins like Nazis studying prisoners against their will and in the US and scientists who studied the untreated progression of syphilis in black patients in Tuskegee, Alabama from the 1930s-1970s. In these and other cases, the welfare of the patient (who is called a subject once they are part of a research study) wasn’t considered AT ALL and what the subjects had to endure was truly awful.

To avoid this from happening in the future, in 1974 the government passed the National Research Act, which resulted in the Belmont Report. From this, three ethical principles were developed in the treatment of research subjects:

  • Respect for persons.  This respect includes allowing them to make their own informed decisions about participating in the research.  This also means that the researcher conducting the study needs to be honest and not try to deceive or coerce patients into participating in the study. For example, the researcher can’t tell the patient that the research will be painless and cure their disease if they know it won’t.
  • Beneficence: Basically this ensures that the researchers do no harm to the research participants – for example, like the harm done during WWII or in untreated syphilis patients.
  • Justice:This is to avoid taking advantage of the patient or a vulnerable patient population.  For example, there are special rules to prevent taking advantage of prisoners or children. This principle also tries to make sure that all research participants receive benefit equally.

protocol for IRB reviewThese ethical principles have been developed into processes that are regulated by the Food and Drug Administration (FDA) and Department of Health and Human Services (specifically Office for Human Research Protections). How does the government make sure these regulations are followed?  Any institution that is performing human subject research has to obtain a Federalwide Assurance, which essentially registers the hospital or university with the government and assures the government that the hospital will follow the ethical rules and guidelines to conduct this research.

For each project or clinical trial involving human subjects, the investigator needs to put together a proposal – what we call a protocol.  This protocol includes information about exactly what is going to be done to the subjects, what the risks are, what the alternatives are for treatment, and how the subject’s safety and confidentiality will be safeguarded. This protocol is the sent to the IRB along with LOTS of other documents about how the patient will be informed about the research (in Informed Consent Form), whether or not the investigators have been trained to perform the research, and information about the drug or device being used.

The IRB is responsible at individual institutions for making sure that patients who become subjects in human subjects research are treated with respect, beneficence and justice while also decreasing the potential risks and letting the patient know what these risks are. The IRB reviews each new protocol (which is exactly what I am doing this weekend!) and at the IRB meeting (which is once a month from 7-9AM), the investigators present their protocol.  The IRB members then ask questions to the investigator and discuss the research after the investigators leave the room.  What do we discuss? It’s confidential for individual studies, but we may talk about how the study is being performed and identify possible problems with the study. We may also talk about the informed consent (what the patient reads to learn about the study – more on that in the next post) and if it accurately explains the research and the risks. We then can vote to approve the study, to send the protocol back to the investigator to answer questions or modify the protocol or to reject the study.

After the study has been approved, the IRB is also responsible for monitoring active research projects.  For example, we receive annual reports that let us know how many people have decided to participate in the study. We also monitor “adverse events.” Adverse events (or AEs) are any event that isn’t anticipated.  This can be anything from nausea to a broken leg to a rash to a missed appointment to death (death is considered a serious adverse event). Whenever an AE happens, the IRB is informed so that if it seems like there are too many of one type of AE, we can take measures to avoid them or tell the subject about an additional risk or shut the research project down.

My participation on the IRB is a responsibility I take seriously because I want any patient who comes to the facilities I work at to understand the research that may be made available to them.  And this understanding includes knowing what the research is all about and what risks the research entails. This is why I’m spending my holiday weekend reviewing research protocols for the IRB.

The Cancer Genome Atlas Project (TCGA): Understanding Glioblastoma

TCGAIn 2003, Cold Spring Harbor Laboratory (CSHL) and researchers around the world celebrated the 50th Anniversary of the discovery of the structure of DNA by Jim Watson and Francis Crick.  I was a graduate student in the Watson School of Biological Science at CSHL, named after James Watson who was the chancellor of the CSHL, and in 2003, I participated in (and planned!) some of the 50th anniversary events. Coinciding with this celebration was a meeting about DNA that brought world-renowned scientists and Nobel Prize winners from around the world to CSHL to celebrate how much had been accomplished in 50 years (including sequencing the human genome) and to look to the future for what could be done next. That meeting was the first time I had heard about the Cancer Genome Atlas Project. At this point, the TCGA (as the project was affectionately called) was just a pipe dream – a proposal by the National Cancer Institute and the National Human Genome Research Institute (two institutes in the National Institutes of Health – the NIH).  The idea was to use DNA sequencing and other techniques to understand different types of cancer at the genome level. The goal was to see what changes are happening in these cancer cells that might be exploited to detect or treat these cancers.  I remember that there was a heated debate about whether or not this idea would work. I was actually firmly against it, but now with the luxury of hindsight, the scientific advances of the TCGA seem to be clearly worth the time and cost.

The first part of the TCGA started in 2006 as a pilot project to study glioblastoma multiforme, lung, and ovarian cancer. In 2009, the project was expanded, and in the end, the TCGA consortium studied over 33 cancer types (including 10 rare cancers).  All of the data that was made publically available so that any results could be used by any scientist to better understand these diseases. To accomplish this goal, the TCGA created a network of institutions to provide the tissue for over 11,000 tumor and normal samples (from biobanks including the one that I currently manage).  These samples were analyzed using techniques like Next Generation Sequencing and researchers used heavy-duty computing power to put all of the data together. So what did they find? This data has contributed to hundreds of publications, but the one I’m going to talk about today is the results from the analysis of the glioblastoma multiforme tumors.

Title: Comprehensive genomic characterization defines human glioblastoma genes and core pathways published in Nature in October 2008.

Authors: The Cancer Genome Atlas Network

gbmBackground: Glioblastoma is a fast-growing, high grade, malignant brain tumor​ that is the most common brain tumor found in adults.  The most common treatments are surgery​, radiation therapy​, and/or chemotherapy (temozolomide​). Researchers are also testing new treatments such as NovoTFF, but these have not yet been approved for regular use. However, even with these treatments the median survival for someone diagnosed with glioblastoma is only ~15 months.  At the time that this study was published, little was known about the genetic cause of glioblastoma – a small handful of mutations were known, but nothing comprehensive. Because of the poor prognosis and lack of understanding of this disease, the TGCA targeting it for a full molecular analysis.

Methods: The TCGA requested tissue samples from glioblastoma patients from biobanks around the country. They received 206 samples that were of good enough quality to use for these experiments.  143 of these also had matching blood samples.  Because the DNA changes in the tumor only happen in the tumor, the blood is a good source of normal, unchanged DNA to compare the tumor DNA to. To these samples, the study sites did a number of different analyses:

  • They looked at the number of copies of each piece of DNA. This is called DNA copy number, and copy number is often changed in tumor cells (see more about what changes in the number of chromosomes can do here)
  • They looked at gene expression.  The genes are what makes proteins, which do all of the stuff in your body.  If you have a mutation in a gene, it could change the protein so that it contributes to the development of cancer.
  • They also looked at DNA methylation.  Methylation is a mark that can be added to the DNA telling the cell to turn off that part of DNA.  If there is methylation on gene that normally stops a cell from growing like crazy, that methylation would turn that gene off and the cell could grow out of control.
  • In a subset of samples, they performed next generation sequencing to know the full sequence of the tumor genomes.

Results and Discussion: From all of this data, the researchers found  quite a bit.

  • Copy number results: There were many differences in copy number including deletions of genes important for slowing growth and duplications of genes the told the cell to grow more.
  • Gene expression results: Genes that are responsible for cell growth, like the gene EGFR, were expressed more in glioblastoma tumor cells.  This has proven to be an interesting result because there are drugs that inhibit EGFR.  These drugs are currently being tested in the clinic to see if this EGFR drug is a good treatment for patients with a glioblastoma that expresses a lot of EGFR.
  • Methylation results: They found a gene called MGMT that is responsible for fixing mutated DNA was highly methylated.  This mutation was actually beneficial to patients because it made them more sensitive to the most common chemotherapy, temozolomide.  However, this result also suggests that losing MGMT methylation may cause treatment resistance.
  • Sequencing results: From all of the sequencing they created over 97 million base pairs of data! They found mutations in over 200 human genes. From statistical analysis, seven genes had significant mutations including a gene called p53, which usually prevents damaged cells from growing, but when mutated the cell can more easily grow out of control
glioblastoma_pathways

This is the summary figure from this paper that shows the three main pathways changed in glioblastoma and the evidence they found to support these genes’ involvement. Each colored circle or rectangle represents a different gene. Blue means that the gene is deleted and red means that there is more of that gene in glioblastoma tumors.

Bringing all of this data together, scientists found three main pathways that lead to cancer in glioblastoma (see the image above for these pathways).  These pathways provide targets for treatment by targeting drugs to specific genes in these pathways. Scientists also identified a new glioblastoma subtype that has improved survival​. This is great for patients who find out that they have this subtype!  Changes in the methylation also show how patients could acquire resistance to chemotherapy. Although chemotherapy resistance is bad for the patient, understanding how it happens allows scientists to develop drugs to overcome the resistance based on these specific pathways.

Although this is where the story ended for this article, the TCGA data has been used for many more studies about glioblastoma.  For example, in 2010, TCGA data was used to identify four different subtypes of glioblastoma: Proneural, Neural, Classical, and Mesenchymal that have helped to tailor the type of treatments use for each group. For example proneural glioblastoma does not benefit from aggressive treatment, whereas other subtypes do. Other researchers are using the information about glioblastoma mutations to develop new treatments for the disease

To learn more about the Cancer Genome Atlas Project, check out this article “The Cancer Genome Atlas: an immeasurable source of knowledge” in the journal or watch this video about the clinical implications of the TCGA finding about glioblastoma

Personalized Medicine: A Cure for HIV

Personalized Medicine – finding the right treatment for the right patient at the right time – is quickly becoming a buzzword both in the medical field but also to the public. But is it just hype? No!  I discussed a number of examples of how personalized medicine is currently be used in breast cancer in a previous post. In this and future posts, I’ll talk about a few fascinating emerging examples of the promise of personalized medicine.  These are NOT currently being used for patient treatment as part of standard of care, but could be someday.

HIV

HIV lentivirus

The Human Immunodeficiency Virus (HIV), the cause of AIDS, is a virus that attacks the immune system.  This attack prevents immune cells from fighting other infections.  The result of this is that the patient is more likely to acquire other infections and cancers that ultimately kill them.  When first discovered in the early 1980s, HIV infection was a death sentence. Untreated, survival is 9 to 11 years.  In the past 30 years, antiviral treatments have been developed that, when taken as prescribed, essentially make HIV infection a chronic disease, extending life to 25-50 years. But there is no cure for HIV, and as of 2012, over 35.3 million people were infected with the virus.

The lack of a vaccine to prevent the disease or of a cure to treat those infected isn’t because no one is trying. Since the virus was identified as the cause of the disease, scientists have been working to find a prevention or cure (along with developing all of the antiretroviral drugs that delay/treat the disease). I’m not going to discuss all of this interesting research (though it is worthy of discussion), instead I’m going to talk about one patient, Timothy Ray Brown, who was cured of HIV/AIDS through a stroke of genetic understanding and luck!

Brown was HIV positive and had been on antiretroviral therapy for over 10 years when he was diagnosed with leukemia in 2007. His leukemia – Acute Myeloid Leukemia (AML) – is caused by too many white blood cells in the bone marrow, which interferes with the creation of red blood cells, platelets and normal white blood cells. Chemotherapy and radiation are used to treat AML by wiping out all of the cells in the bone marrow – both the cancer cells and the normal cells. Brown’s doctors then replaced the cells in the bone marrow with non-cancerous bone marrow cells of a donor.  This is called a stem cell transplant, and it is commonly used to treat leukemia – often resulting in long term remission or a cure of the disease.

But the really cool part of this story isn’t the treatment itself.  Rather it’s that that Brown’s doctor selected bone marrow from a donor that had a mutation in the gene CCR5. So what? The CCR5 protein is found on the outside of the cells that the HIV virus infects. CCR5 is REQUIRED for the virus to get inside the cell, replicate, and kill the cell. Without CCR5, HIV is harmless. There is a deletion mutation in CCR5 called delta32 that prevents HIV from binding to the cell and infecting it.  Blocking HIV from getting into the cell prevents HIV infection.  In fact, it’s been found that some people are naturally resistant to HIV infection because they have this deletion. Two copies of the gene are found in 1% of the Caucasian population, and it’s thought that this mutation was selected for because it also prevents smallpox infection.
HIV_ccr5So Brown’s doctors repopulated his bone marrow with cells that had the CCR5-delta32 mutation.  This didn’t just cure his leukemia but it also prevented the HIV from infecting his new blood cells, curing his HIV. He is still cured from HIV today!

What does this mean for others who are infected with HIV? Is a stem cell transplant going to work for everyone?  Unfortunately, no. This mutation is very rare, so finding donors with this mutation isn’t feasible.  Plus, this is a very expensive therapy that comes with risks such as graft-versus-host disease from the mismatch between the person receiving the transplant and the transplanted cells themselves. However, there are possible options to overcoming these challenges, including “gene editing.” In this method, T cells from HIV-positive patients would be removed from the body and then gene editing would be used to to make the CCR5-delta32 mutation in these cells.  These cells could then be re-introduced into the patient.  With the mutation, HIV won’t be able to infect these T cells, which would hopefully cure the disease, while avoiding some of the major graft-versus-host side effects. A small clinical trial tested this idea in 2014 (full article can be found in the New England Journal of Medicine), and HIV couldn’t be detected in one out of four patients who could be evaluated. Although this is a preliminary study using an older gene-editing technique, it shows promise for “personalized gene therapy” to potentially cure HIV.

Book Club: The Immortal Life of Henrietta Lacks

The_Immortal_Life_Henrietta_Lacks

Thanks to Wikipedia for the image

In 2002, one of my first set of experiments in graduate school was treating the prostate cancer cell line (named DU145) with a chemotherapeutic drug and comparing how these cells responded to how HeLa cells responded to this chemotherapy. Little did I realize at the time that 51 years earlier, these cells were removed from a poor black woman named Henrietta Lacks without her even knowing. She subsequently died, but her cells have lived on for over 60 years being used by researchers around the world to better understand cancer. It’s estimated that over 60,000 research papers have used HeLa cells (I just searched the literature for “HeLa” and found over 83,000 results). HeLa cells helped to develop the polio vaccine (HeLa cells were easily infected by polio, and therefore ideal to test the vaccine).  In 2013, HeLa cells were the first cell line to have its genome fully sequenced (the genome of HeLa cells is a hot mess with more than 5 copies of some chromosomes – likely caused by the number of times that the cells have divided over the past 60 years).  In fact, HeLa cells are so popular and so widespread that they have been found to be contaminating a large percentage of the OTHER cell lines that researchers are using (for example, the bladder cancer cell line KU7 was found to exclusively be HeLa cells in one research lab).

With all of this activity surrounding HeLa cells, you may think that she is famous and her family has received recognition from her donation.  However, as so artfully described in Rebecca Skloot’s “The Immortal Life of Henrietta Lacks” these cells were taken and grown without her consent and her family had no idea that Henrietta was was “immortal” through her cells growing in las around the world. Skloot describes the moral and ethical issues surrounding how these cells were obtained while weaving a story about Henrietta Lacks and her family’s life and discovery of HeLa cell’s fascinating rise to prominence.  Although the story is interesting to a scientist and a biobanker, the book is definitely written in such a way that the public will completely understand the scientific significance.

Growing tumors outside the body to kill the tumor still inside

To understand how to kill a tumor, you have to study the tumor. Historically, much of how scientists understand tumors comes from removing a tumor from a patient’s body, putting Cell_Cultureit in a plastic dish (called a petri dish), and studying whatever cells are grown in this dish. You may be familiar with the book “The Immortal Life of Henrietta Lacks” by Rebecca Skloot. This book talks about HeLa cells, which are cells that were taken from Henrietta’s cervical cancer, grown in a dish, and propagated for the past 60+ years as what is called a “cell line“.  These cells grow and divide indefinitely, and have been propagated and transferred from lab to lab to be studied.  HeLa cells are one of the most famous and most-researched cells that have helped scientists better understand cancer. HeLa cells are not the only cell line that exists or has been used to study cancer.  There are cell lines from lung cancer tumors, prostate cancer, brain cancer, and most other major cancers. However, there are a few problem with using cell lines to understand and treat cancer.

  1. Cell lines are EXTREMELY hard to create.  As you may imagine, a plastic dish is nothing like the environment inside the body that the tumor was removed from.  In the petri dish the cells are put into “media,”t he liquid that is used to feed the cells in the petri dish, and this media is also nothing like the nutrients and other growth factors feeding the tumor inside the body. Because of this unnatural environment, some of the tumor cells die – and in many cases mostor all of the tumor cells die.
  2. The cells that are left in the petri dish do not accurately represent the tumor anymore. A tumor isn’t a whole bunch of identical cells, but rather a tumor contains a lot of genetically different cells.  Scientists call this tumor heterogeneity. This is one of the reasons why drug resistant cells emerge after treating a tumor with drugs (like in the case of melanomadescribed in a previous post).  There are already drug resistant cells inside the tumor that don’t die when treated with drug.  Unfortunately, not all of these different cells in the tumor will live in a petri dish, so only a selected type or types of cells will live and can be studied.
  3. Even though cell lines had been the most useful tool in the past to understand cancer biology, they are not at all useful in understanding the EXACT tumor from a particular person. What does this mean? For example, drugs that kill HeLa cells in a petri dish might not work to kill another person’s cervical cancer because the genetic cause of that cervical cancer is different. In personalized medicine, the goal is to identify the drugs that will work to kill a particular patient’s tumor. Because of this, cell lines just aren’t good enough.

Scientists have been working on a number of solutions, and I’ll talk about four:

  1. Biobanking. A biobank collects excess tumor tissue from patients who are having a
    liquidnitrogenfreezers

    Where tumor tissue is stored in a biobank before researchers use it

    tumor removed as part of a surgery.  This tissue is immediately preserved by freezing and can then be used by researchers to study that particular tumor or many tumors of a particular type (e.g., lung cancer).  The disadvantage to this is that the tumor sample isn’t an unlimited resource. Once the tissue has been used up – it’s gone. The remaining examples all focus on growing the tumor tissue so that it can be propagated and used for many experiments.

  2. Modified cell line growth. HeLa cells were not grown in any special way, but researchers at Georgetown Universityhave found ways to grow tumor cells in a petri dish  that are identical to the tumor and nearly all tumors can grow under these conditions. So what are these conditions?  The researchers grow cells on top of a layer of mouse cells called feeder cells because they provide the cell-based nutrients to “feed” the tumor and allow it to grow.  They also use a particular inhibitor that allows the cells to grow indefinitely. They have created these modified cell lines from different types of tumors, from frozen biobanked tumors, and from as few as 4 live cells.  Even though this system, is better, it still doesn’t replicate the 3D architecture of a tumor…
  3. cancer organoids

    Cancer organoids. Notice the 3D clumps of cells after 217 days of growth. Thanks to the Kuo lab for the image

    Organoids. As you would expect the word to mean, an organoid is a mini 3D organ bud grown in a dish. Don’t imagine a teeny tiny beating heart.  These organoids are just clumps of cells, but an organized clump of cells that can help better understand cells and organs. The discovery of how to create organoids was so interesting that it was a 2013 Big Advance of the Year by The Scientists magazine. Scientist have also found a way to grow cancer cells into these 3D organoid structures. With tumor organoids, researchers can both study the genetics of the tumor (like you can with cell lines) as well as how the tumor behaved in a 3D environment that is more similar to what the tumor encounters in the body.  But what if we could do even better?

  4. Patient-derived xenograftsare when tumor tissue is taken directly from a patient’s tumor and put directly into a mouse.  Why would this be so awesome? The environment inside a mouse is more similar to the environment that the tumor is used to inside a person’s body.  The cells are less likely to die because they aren’t living in unnatural plastic. Also, a whole piece of tumor can be implanted into the mouse, maintaining the tumor cells connections to neighboring cells, which are critical for the tumor cells to communicate with one another for survival.

With all of these systems available to study tumors from a specific patient, what are scientists actually doing with these cells? In some cases, they are being used to sequence the genomes of the tumors to identify mutations that may be causing the tumor. If a tumor can be grown so that there is a lot of it, the tumor cells themselves can also be used to test treatments either in a dish or inside of a mouse. Imagine a cancer patient getting their tumor removed, part of the tumor is grown in one of the ways described above. Then the tumor is exposed to the top 10, or 50 or 100 anti-tumor drugs or combination of drugs to see what kills the tumor. This drug or combo of drugs can then be used to treat the patient. There are companies that are currently working on doing exactly this (check out Champions Oncology) so this “big dream” may soon become a cancer patient’s more promising reality.

 

The best week ever – Nobel Prize week!

nobelLast week was one of my favorite weeks of the year – Nobel Prize week. Some people wait for the Emmys or the Superbowl or Christmas.  I wait for the Nobels. To be fair, I care most about the science Nobels – Physics, Chemistry and Physiology or Medicine, though one cannot ignore the amazing accomplishments of the winners in Literature, Peace, and Economics. Every year, I try to guess who may win – though Thomson Reuters and others are far more scientific about their guesses than I am.  And each morning of Nobel Week, first thing I do is check the news on my phone to see who won, what for and whether or not I know them (this year – no).  Let’s talk about who won the science awards this year and what amazing discoveries they won for.

Physiology or Medicine. A lot of attention has been given to infectious diseases this year with the huge Ebola outbreak in western Africa.  Although tens of thousands of people were infected and died, other infectious diseases are even more widespread and affect millions of people a year. Malaria is a parasitic disease transmitted by mosquitoes that 3.4 billion people are at risk of contracting and that kills over 450,000 people per year. Parasitic worms are also rampant in the third world, can affect up to a third of the human population, and cause such diseases as river blindness.  This is the second most common cause of blindness by infection, with 17 million people infected and 0.8 million blinded by the disease.  The three winners of the Nobel for Physiology or Medicine this year discovered novel treatments for these parasitic diseases.  William C. Campbell and Satoshi Ōmura for roundworm parasites and Youyou Tu for malaria, saving hundreds of thousands of lives each year.

Chemistry. This is by far my favorite award this year because it is directly related to how humans safeguard their DNA, but also why when this safeguard does work, that we get cancer.  Awarded to Tomas Lindahl (UK), Paul Modrich (USA), and Aziz Sancar (USA), this Nobel celebrates the discovery of the mechanism of DNA repair. I’ve discussed in this blog how UV and other environmental factors can cause mutations in DNA, and with too many mutations, people can develop cancer or other diseases.  However, the genome doesn’t mutate out of control because cell contain the machinery that is always working to fix any DNA damage using DNA repair mechanisms. It’s like a NASCAR race, where the car is always being monitored, wheels replaced, and minor problems fixed by the pit crew.  DNA repair is the genome’s pit crew and these three scientists figured out three different ways that the cells monitors and fixes the DNA depending on the type of damage that has occurred.

Physics. We all know I’m not a physicist, but I’ll try my best. The Physics Nobel was awarded to Takaaki Kajita of Japan and Arthur B. McDonald of Canada for discovering that neutrinos have mass.  You may remember from high school that atoms are made up of protons, neutrons and electrons. However, scientists now know that there are even tinier parts of an atom called subatomic particles that include the neutrino, fermions and bosons (and others). Other than photons, which are the particles of light, neutrinos are the most numerous subatomic particle in the entire cosmos, so understanding how they work is incredibly important.  These researchers found that the three different types of neutrinos can convert from one to the other. It was predicted by the Standard Model of Physics that these neutrinos wouldn’t have mass, but these scientists also proved that they did. Their studies help to better understand matter and the universe. My favorite reporting of this award was by NPR.

So until next year Nobel Prizes.  I will be waiting with baited breath!