Wednesday, April 26, 2017

Learn about interactions between transcription factors and chromatin modifiers in cardiovascular disease!

Recent review article regarding the interactions between chromatin modifiers
and transcription factors in cardiovascular disease.
Cardiovascular disease development is really complex. Cells that contribute to cardiovascular disease
such as cardiomyocytes, endothelial cells, and vascular smooth muscle cells will behave abnormally (increased cell death, cell division, altered phenotype, etc) downstream of genetic mutations and/or environmental stimuli. Genetic mutations and/or environmental stimuli (for example, high fat diet, smoking, etc) alter the signaling in the cells leading to dysregulated expression of genes. We know that altered signaling promotes changes in transcription factor and chromatin modifier expression, activity and/or function leading to the dysregulated expression of genes in cardiovascular disease. Although scientists have identified several key transcription factors and chromatin modifiers that are important in cardiovascular disease development, the role of the interactions between them are less clear. However, by better understanding the interactions of transcription factors and chromatin modifiers in cardiovascular disease, we will hopefully be able to develop more and better therapeutics in the treatment of cardiovascular diseases. We've recently written a review published in Frontiers in Cardiovascular Medicine that describes some of these known interactions and highlights some of the questions that remain in the field. So check it out to learn more about transcription factor and chromatin modifier interactions in cardiovascular disease! I would love to hear what you think about this topic! Feel free to comment below or send me an email. Also, don't forget to follow me on Twitter!

Wednesday, March 1, 2017

Skin cells can transform into fat cells during wound healing

Schematic of the layers of the skin and its associated
structures. This study found that myofibroblasts near the
hair follicles are able to convert to fat cells.
Image source
The skin serves as a protective barrier against the environment. It is composed of three layers: the outermost, waterproof barrier called the epidermis; the middle dermis layer that contains many cell types that make up connective tissue, hair follicles, and sweat glands; and the deepest subcutaneous layer made up of fat and more connective tissue. When this barrier is broken, the body works quickly to repair itself by stopping bleeding, recruiting immune cells to help clean up and prevent infection, growing new cells, and remodeling of the tissue to return to its normal state. Oftentimes, this repair process results in scarring if the repair happens relatively slowly. In the type of healing in which a scar forms, there are no sweat glands, fat, nerves, or hair follicles. Obviously, this presents a huge concern for patients like burn victims that have a large injury resulting in scarring. By better understanding the process of scarring we will hopefully be able to find better ways to treat these patients.

A recent study published in Science was investigating the cell types involved in wound repair in mice. They happened to notice that new fat cells within wounds were being made near hair follicles surrounding the injury. These fat cells looked like normal fat cells and expressed fat-specific proteins. The scientists wanted to know if the hair follicles were necessary for making new fat cells. To test this, they grew cells from the dermal skin layer (made up of many different cells types) of wounds that contained hair follicles or from wounds that didn’t contain follicles. They found that only the cells from wounds that contained hair follicles became fat cells suggesting that the hair follicles were involved in converting these dermal cells into fat cells. They determined that the fat cells specifically came from a cell type called myofibroblasts that are normally present in the dermal skin layer, but only became fat cells if they were right next to hair follicles. When these fibroblasts were grown in culture with scalp hair follicles, they were able to be converted into fat cells. It turns out, these myofibroblasts near the hair follicles specifically turn on expression of proteins called bonemorphogenetic proteins, or BMPs. These proteins have numerous cellular signaling roles, but in this case they activate a specific protein known as ZFP423 which drives cells to become fat cells during development. When the researchers prevented either BMP or ZFP423 from being increased then the myofibroblasts were also prevented from turning into fat cells.

This study has several potential implications, although future studies are necessary to understand the mechanisms that govern the switch from wound myofibroblasts to fat cells. For example, why are the myofibroblasts that are closest to the hair follicles the ones that are converted into fat cells and how does the wound healing process influence the ability of these cells to convert from myofibroblasts to adipocytes? Nevertheless, these findings demonstrate that cells derived from one cell lineage (e.g. the dermis) can convert to another lineage (e.g. fat cells). With future studies, perhaps we can take advantage of this phenomenon to promote regeneration of tissue rather than scarring following an injury. Moreover, the authors suggest that perhaps one day we could treat patients with disorders involving a lack of fat (e.g. lipodystrophies, aging, etc) by converting myofibroblasts from these patients into fat cells.

For more information on what's discussed in this post, please follow the links throughout or feel free to send me an email!

Wednesday, January 11, 2017

Is RNA splicing the link between nutrient restriction and long lifespan?

A recent study identified a link that may explain how deprivation promotes longevity- RNA splicing! Before being translated into protein, recently transcribed mRNA undergoes splicing, an important physiological process that has been implicated in disease development when it doesn’t happen correctly. During splicing, introns are removed from the pre-mRNA and a specific combination of exons are joined to form a mature mRNA. There are several proteins that work together during splicing. Differential expression of these RNA splicing proteins has been associated with longevity, or a long lifespan. However, until this study, the role of RNA splicing (if any) in longevity in dietary-restricted organisms was unclear.
Caenorhabditis elegans that are expressing green and red
fluorescent reporters.
Image source

To answer this question, this group used the nematode Caenorhabditis elegans (C. elegans) as a model organism. A model organism is a widely studied species that is typically easy to breed, there is a lot known about it, and has many experimental advantages.  In this case, C. elegans is an ideal model to study aging because they have short lifespans and a defined pattern of development. The particular strain this group used had a fluorescent reporter to signify splicing. Therefore, when a specific mRNA known as ret-1 (RNA polymerase III subunit) was spliced one way the cells were one fluorescent color, but if it was spliced a different way then the cells were another color. This allows the researchers to quickly and easily identify if splicing occurred and assign a value to the splicing event.

In 5 day old C. elegans (when they are still considered young), exon 5 of ret-1 remained in the mRNA so the majority of the worm was green establishing a “young” pattern of alternative splicing. From day 7 onward, exon 5 gets spliced out (i.e. removed) from a larger number of cells such that more cells of the worm are red. However, this splicing occurred at different rates within and between individual worms giving a lot of variation to the amount of green compared to red in the worms. This suggests that aging results in differential alternative splicing which occurs at different rates between individual worms. Interestingly, when these worms were nutrient restricted, not only did they live longer, but they also exhibited the more “young” pattern of alternative splicing (i.e. more cells of the worms were green).

To confirm that this “aged” pattern was due to splicing, researchers sorted 6 day old worms that were fed a normal diet into two groups based on if they were mostly red (“aged” pattern) or mostly green (“young” pattern). They found that the worms that were sorted into the green group had a longer lifespan than those in the red group. These findings demonstrate that worms fed a normal (non-restricted) diet exhibited a faster decline in splicing efficiency.

These authors also identified proteins involved in splicing that also promoted longevity in the worms. One of the proteins they focused on is called splicing factor 1 (SFA-1). Dietary restriction no longer extended worm lifespan when they knocked SFA-1 down. Moreover, knocking down SFA-1 prevented age-related changes in ret-1 splicing while overexpressing SFA-1 increased lifespan. Together, these results suggest that SFA-1 promotes increased lifespan after dietary restriction through regulating RNA splicing.

This study identifies an interesting link between RNA splicing, aging, and dietary restriction. However, whether this connection holds in higher order animals like humans is unknown, but will likely be an area of future investigation. If it a
lso exists in humans, it could have interesting long-term implications for delaying aging and even in treatment of diseases that are known to be caused by splicing defects.


If you find this summary interesting, you can read the full story here or follow links throughout the article! Don’t forget to follow this blog and follow me on Twitter! Feel free to email me if you have any questions or comments! I would love to hear them! 

Tuesday, December 20, 2016

Clinical study identifies potential benefit to using combined lipid-lowering therapy to reduce arterial plaque

Image of a coronary artery that supplies the heart with blood.
There are two images showing a coronary artery with plaque built
up and another in which the plaque has burst. Lipid lowering drugs
help to prevent plaque deposition in arteries like the coronaries.

Image source
Cardiovascular disease is the leading cause of death in the U.S. and worldwide. There numerous types of cardiovascular diseases including high blood pressure, heart failure, or coronary artery disease. Coronary artery disease is caused by the build-up of a fatty, cholesterol-rich substance called a plaque in the coronary artery wall. This disease process is known as atherosclerosis (In Greek, “athere” means “gruel” and “skleros” means “hard”). The build-up of plaque in the arteries can continue to grow and harden or, alternatively, the plaque can burst causing a clot. Either of these can lead to artery blockage and, subsequently, decreased blood flow to tissues. Decreased blood flow to tissues like the heart or brain can lead to a heart attack or stroke, respectively.


The exact cause of atherosclerosis isn’t really known (but is an active area of research for labs like mine!), but a contribution of one or more genetic or environmental factors can increase the risk of atherosclerosis progression. One example of a factor that contributes to atherosclerosis progression is high levels of circulating cholesterol, specifically low-density lipoproteins, or LDL cholesterol. Therefore, many of you have probably had your LDL cholesterol levels measured as part of a routine physical since it is a known risk factor for atherosclerosis development. Not all cholesterol is bad though. In fact, your body requires cholesterol to make parts of cell membranes, hormones, and vitamins. However, cholesterol alone can’t just flow through your blood stream. It needs to be packaged up within lipoproteins like LDL or high-density lipoprotein (HDL) to get to where it needs to be in your body. Healthy levels of both types of these lipoproteins (LDL and HDL) is important for normal function. Even though both types of lipoprotein are required, HDL is considered good because it helps to pick up LDL cholesterol from the circulation and bring it back to the liver where it is broken down and passed from the body whereas LDL contributes to plaque buildup.

It is very important to monitor and control LDL levels to reduce risk of cardiovascular disease. In addition to diet and exercise or in many individuals who are unable to control their LDL levels through lifestyle changes, using a class of drugs called statins is highly effective in reducing circulating LDL levels, atheroma burden and cardiovascular events. Statins reduce LDL levels by inhibiting the enzyme that makes LDL, known as HMG-CoA reductase. However, even with statins, some individuals are unable to sufficiently lower their LDL levels, experience negative side effects with effective doses, or still experience cardiovascular events. Therefore, there is still a need to develop additional LDL-lowering therapies for this group of individuals.

In fact, studies have identified that inhibiting another protein called proprotein convertase subtilisin kexin type 9 (PCSK9) can further reduce LDL levels with or without the concurrent use of statins. PCSK9 is an enzyme that prevents the LDL receptor from returning to the surface of liver cells. If the LDL receptor is unable to get to the surface of liver cells, then instead of binding to the receptor and getting removed from the blood by the liver cells, LDL stays floating in the blood and can contribute to plaque formation. Therefore, using an inhibitor of PCSK9 allows the LDL receptor to get to the cell surface and continue removing LDL from the blood to prevent plaque development. Although we know that inhibiting PCSK9 with anti-PSCK9 antibodies lowers LDL levels, it is unknown whether inhibiting PCSK9 reduces the rate of coronary artery disease or if combining PCSK9 inhibitors with statins (HMG-CoA reductase inhibitors) to achieve very low levels of LDL has a greater benefit than using statins alone. Fortunately, a recent study published in the Journal of the American Medical Association conducted a clinical trial to investigate this question.

This large clinical trial was conducted by several investigators at various centers throughout the world including in North America, Europe, South America, Asia, Australia, and South Africa in collaboration with Amgen Inc. The clinical study was limited to participants older than 18 years of age who were on a statin with controlled LDL levels, but with at least one coronary artery blockage of at least 20% and cardiovascular disease risk factors. Participants were randomly assigned into placebo (receiving a “fake” treatment) or an anti-PCSK9 treatment group with a drug called evolucumab (an FDA approved drug by Amgen). Neither the researchers nor the participants knew if a participant was receiving the treatment or placebo which is referred to as a double-blind clinical trial.  After being split into treatment or placebo group, each participant received an ultrasound to determine the plaque area. Participants were followed over 78 weeks and the change in plaque area was determined and measurements of lipids like LDL and cardiovascular events were recorded.

They found that anti-PCSK9 treatment, in addition to statins, reduced blood LDL by about 40 percent as well as increases in HDL. Additionally, participants who received treatment had a 5.8mm3  reduction in plaque volume (compared with 0.9mm3 in placebo-treated patients) and more patients that received anti-PCSK9 treatment with statins exhibited this decrease. They also report that participants who received both anti-PCSK9 and statin treatments had fewer adverse cardiovascular outcomes (12 percent in the treated group compared with 15 percent in the placebo group which received only a statin). Importantly, anti-PCSK9 treatment was well-tolerated with no differences in side effects compared with the placebo group.

The results from this clinical have exciting implications for combined use of anti-PCSK9 and statin therapy in promoting plaque regression and reduction of cardiovascular events. They report that patients receiving anti-PCSK9 treatment in addition to statins have reduced progression of atherosclerosis compared with placebo groups. They suggested one possible explanation for enhanced benefit of combined therapy may be that PSCK9 levels increase following statin treatment. Therefore, inhibiting PCSK9 in addition to statins can further reduce circulating LDL. Although these results are promising, further safety tests and larger clinical trials are necessary to ensure there are no adverse effects of combined treatment. Additionally, it would be interesting to determine if even more patients exhibit atherosclerosis regression with extended length of treatment, or if long-term treatment will be associated with increased side effects.


If you’re interested in reading more about atherosclerosis, LDL and PCSK9, or this study, follow the links throughout the post! Please contact me with any questions or comments!

Thursday, October 27, 2016

Study provides first evidence of tRNA demethylase that can regulate protein synthesis

Cartoon of tRNA "clover" within a ribosome. The top isbonded with an amino acid
and the bottom matches with mRNA template. The ribosome aids in
connecting amino acids together to form protein. Recent study found that
tRNAs can be modified by ALKBH1 to regulate this process.

Image source
Proteins are built from amino acids joined together into long chains in the process of translation. Amino acids are attached in the correct order by ribosomes that use messenger RNA (mRNA) as a template. Transfer RNAs (tRNAs) carrying a specific amino acid bind within the ribosome to a complementary region of the mRNA. If the tRNA matches to the region of mRNA, the amino acid it’s carrying gets incorporated into the lengthening amino acid chain. tRNAs are folded into a clover-shaped structure which is critical to their function. Specific regions at the top of tRNA “clover stem” bind to the amino acid and a specific region in the bottom of the tRNA “clover” interacts with the mRNA. Therefore, if the specific structure of the tRNA is disrupted, it may no longer be able to interact with the ribosome or mRNA properly or carry the correct amino acid. Interestingly, it has been shown that tRNAs can be modified to influence their structure and, therefore, function.

Since tRNAs are nucleic acids, they can also be post-translationally modified similar to how DNA bases can be methylated. Several different tRNA bases can be methylated to change the stability of the tRNA structure, allow amino acids to be attached, or alter how the tRNA binds to the mRNA template. A study published in Cell last week identified a new role for methylation of tRNA- regulation of translation itself! This group at the University of Chicago found that an enzyme called ALKBH1 binds to and demethylates tRNA inside of cells. ALKBH1 belongs to a family of enzymes that are known to work on DNA although a lot of their roles, including that of ALKBH1, are unclear. A related family member, ALKBH5, had previously been shown to remove methyl groups from adenine of RNA. This is the first study to demonstrate that ALKBH1 is an RNA demethylase that seems to specifically modify tRNA. They report that knocking down ALKBH1 leads to methylation of the tRNA involved in starting translation. This stabilizes the initiating tRNA and promotes the start of translation and cell division. They also found that decreasing levels of ALKBH1 leads to increased methylation of specific tRNAs and increases translation elongation, or growth of the amino acid chains.

This is the first study to identify an enzyme that demethylates tRNA in order to influence gene expression by regulating translation. Studies on RNA modifications and the enzymes that add or remove these marks are relatively new. Although this study determined that ALKBH1 seems to prefer tRNA as a substrate, it will be interesting to see if these findings hold with improved methods to identify RNA modifications and the enzymes that add or remove them. Furthermore, this study determined that demethylation of tRNA by ALKBH1 regulates translation. Future studies should continue to elucidate the roles for tRNA (and other RNA) modifications in regulation of gene expression. Finally, determining if and what role RNA modifying enzymes like ALKBH1 have in development and disease will be an important area of future research.

If you would like to read more about this study or learn more about RNA modifications, please follow the links below! Please feel free to contact me with any comments or questions!

References:

Tuesday, October 4, 2016

Yoshinori Ohsumi receives 2016 Nobel Prize in Physiology and Medicine for his work on autophagy!

Congratulations to Dr. Yoshinori Ohsumi,
recipient of the 2016 Nobel Prize in
Physiology and Medicine for his work
on autophagy!
After an unfortunately long break in the blog action with the end of summer and start of the new Nobel Prize recipients!
school year, I thought I’d update with the latest news in the world of science- announcements of

Congratulations to Dr. Yoshinori Ohsumi from Japan who received the 2016 Nobel Prize in Physiology or Medicine for his work on autophagy!

Autophagy (Greek for self (auto) eating (phagein)) is a normal process that cells use to take apart and throw away cellular parts that no longer work or are no longer necessary- the cell’s very own waste disposal system. This process occurs in organelles called lysosomes which are small vesicles within the cells that contain the proteins that break down a variety of molecules including other proteins, nucleic acids, carbohydrates, lipids-you name it (side note: the scientist who discovered lysosomes was also awarded the Nobel Prize back in the 1970’s!). There are a few ways autophagy can occur: 1) through macroautophagy, 2) microautophagy, or 3) chaperone-mediated autophagy. Macroautophagy occurs when unwanted proteins or organelles get packaged up within a double membrane called an autophagosome. This structure makes its way to the lysosome where they combine and all the damaged, unwanted, or unused components in the autophagosome get broken down by the proteins within the lysosome. In the second autophagy pathway, microautophagy, these unwanted structures or cellular components get eaten up by the lysosome directly and subsequently broken down. Finally, the third autophagy pathway is less straightforward. In chaperone-mediated autophagy, chaperones (specifically ones containing a protein called hsc70) recognize a specific site found on select proteins that enable them to be escorted by the chaperone complex to the lysosome.

There are many important roles for autophagy in keeping a cell running like it is supposed to. Obviously, autophagy keeps the cell clean and gets rid of any unnecessary stuff which is important in protecting the cell from damage. Interestingly, it’s been suggested that if this process becomes dysregulated leading to build-up of unwanted materials and subsequent cell damage it can accelerate aging! Autophagy is also important in breaking down proteins into smaller components that the cell can then use for other processes. This becomes especially important in starvation conditions when the cell may not be getting the necessary nutrients and stimuli it needs from the outside to function properly. Degradation of foreign invaders like viruses or bacteria in the cell is regulated through autophagy. This leads to the destruction of the foreign body and helps the cell protect itself from infection. Finally, studies also suggest that autophagy is involved in a normal type of cell death called apoptosis, or programmed cell death (vs necrosis which is cell death due to injury). However, it is unknown if autophagy initiates this programmed cell death or if it just occurs as part of the process. The important role for autophagy in the cell processes described here (and there are more not described here and probably more to be identified) suggests that autophagy is also important in many diseases. Indeed, it seems there are roles for this autophagy in cancer, arthritis, and Parkinson’s disease.


Dr. Ohsumi has an interesting story leading up to the discovery of autophagy in that it was more on the unremarkable side- he didn’t make all these amazing discoveries or revolutionize medicine at a young age. In fact, he was in his 40’s when he conducted the Nobel Prize-winning research. Nevertheless, that quickly changed as Dr. Ohsumi did remarkable work in identifying the genes and mechanisms that regulate autophagy that really established autophagy research as a field and highlighted its importance in physiology and disease. Congratulations, Dr. Ohsumi!  

If you have any questions, comments, or suggestions please let me know in the comments below or feel free to email me! Visit the links below for more information on the topics discussed in the post.

Resources & links for further reading:

Wednesday, July 27, 2016

Using Gene Therapy to Treat Genetic Liver Diseases

An exciting recent study used gene therapy to treat a
pig model of hereditary tyrosinemia type I (HT1).
Image source
Thousands of diseases are caused by genetics. These diseases occur when a mutation (or a change) occurs in the DNA sequence that negatively affects the function of the RNA or protein that is made from the DNA. This category of diseases can be relatively common as in the case of breast cancer, or rare as with hereditary tyrosinemia type I (HT1). HT1, for example, is found in approximately 1 in 100,000 people and occurs when there is a mutation in the gene that produces the fumarylacetoacetate hydrolase (FAH) enzyme. Yes, such a thing exists in your body and has a very important role! FAH is found mostly in the liver and kidneys and breaks down the amino acid tyrosine, one of the building blocks that makes up proteins. In people with the genetic disease HT1, FAH is not as active as it should be so tyrosine doesn’t get broken down very well. As a result, tyrosine levels build up and severely damage the liver, kidneys, and other organs where FAH is found. These patients typically develop severe liver fibrosis, liver cancer, or even liver failure if their disease is left untreated. Treatment of these patients includes a diet low in tyrosine (to keep it from building up) and a drug that helps to break tyrosine down. However, a lot of patients don’t respond well to this treatment option or, even if they respond initially, will still end up with severe liver damage. The only way to cure this disease is a liver transplant (oftentimes, in children) which obviously carries its own set of risks. Therefore, new and more effective treatments are needed for HT1.

Since HT1 is a disease caused by a known mutation in a single gene (FAH), use of gene therapy is an attractive treatment approach. Gene therapy is an experimental technique that alters the gene in the patient’s cells. This can be done either through replacing the mutated gene with a normal copy, getting rid of a mutated gene that isn’t working correctly, or adding in a completely new gene to help fight the disease. Gene therapy remains an experimental treatment approach and is normally only used if there are no other treatment options because there is a lot we don't know about it yet. However, it may prove useful as researchers continue to improve its safety and efficacy. In fact, a group at Mayo Clinic has been working on the use of gene therapy to treat FAH mutations in animal models of HT1.

In a recent study published by this group in ScienceTranslational Medicine, they studied pigs with an FAH mutation that caused the enzyme to be “knocked out” or no longer produced correctly. These pigs, like humans with similar FAH mutations, will develop liver failure. Therefore, it makes them a useful model to study potential treatments like gene therapy. First, this group tried transplanting liver cells (not the whole liver) from a pig with one copy of the normal FAH gene into a pig that had the mutated FAH gene. However, the pig’s symptoms did not improve and none of the liver cells from the healthy pig stayed in the liver of the mutated pig. Next they removed some of liver cells from a different pig with mutated FAH and used a virus to infect the liver cells with a healthy, functioning copy of the FAH gene. Then they put those cells back into the liver of the same pig. Around 3-6 months after transplanting the cells that underwent FAH gene therapy, they found that the transplanted cells stayed in the liver of the pig and there was no evidence of liver damage. After one year, the pigs with the FAH mutation who were treated with the transplanted cells were gaining weight, had lower levels of tyrosine, and had no evidence of liver dysfunction. They found that the transplanted cells repopulated almost the entire liver, there was no evidence of liver cell death, and there was decreased liver fibrosis.

This is an exciting proof-of-principle study. This means that this group demonstrated the potential for non-invasively removing cells from the liver of a patient with a genetic condition affecting the liver, treating the cells outside of the body with a virus carrying a healthy copy of the gene of interest, and then putting them back into the patient’s liver to treat the condition. They demonstrated that using the patient’s own liver cells for gene therapy and then transplanting them is a way to bypass the negative effects of using donor cells. By infecting the cells with the virus carrying the healthy FAH gene, they also bypassed the issues of off-target effects of gene therapy on other cell types. However, because they removed the patient’s own liver cells to use for gene therapy such an approach would not be suitable for other organ systems and cell types that cannot regenerate as easily such as the brain or heart. They also only used a few pigs in their study so this will have to be repeated with a larger group to account for any variation between pigs as might occur in humans. Since they used a virus to introduce the healthy FAH gene into the diseased liver cells with the mutant FAH, more studies will need to be done on the type of virus. These viruses may insert the gene into a location in the genome that introduces its own mutation and set of problems. Finally, before such a study could be performed in humans, more studies on where and how the liver cells are staying transplanted, how they are dividing and taking over the liver, and the toxicity of the virus to cells will need to be performed. However, the present study is another great step toward establishing another therapeutic option for people with genetic disease. Future more studies should be performed on other genetic conditions involving rapidly dividing cells such as blood cells or liver cells.

Have any questions or comments? I would love to hear them! Email me or post in comments below!