Altering the Human Genome

 A 10-year-old boy from Warren County, Jackson, was born with Leber’s Congenital Amaurosis (LCA) \ RPE65, he was treated with the first FDA approved gene therapy drug called Luxturna. This drug is provided to each eye and treats the genetic disease that causes blindness. This would add a working RPE65 gene in place of the mutated genes. With the new working gene, the cells would then begin to produce functioning protein. Jackson's distance vision started off as 20/1000 and after being treated with Luxturna his distance is no 20/80, a major difference and almost complete recovery of his vision. 

This story is crazy to me because I remember this kid from when I was in grade school. He was in preschool when I met him, way before he received this treatment. I had the pleasure of meeting him again years later, after he received the treatment, and he is a brand new person almost. Now, this once small kid in preschool, is in high school and can go about his daily life independently. It is truly remarkable what gene therapy can do, and I cannot wait to see what researchers can make of it in the future. 

The Genetics Behind Diabetes

 Type 1

Up to 0.4% of children will be diagnosed with type 1 diabetes by the age of 30, making it the third most frequent form of pediatric chronic illness. It is brought on by the autoimmune death of beta cells in the pancreas, which leads to total dependence on insulin from outside sources. A genetic risk ratio of roughly 15 is associated with type 1 diabetes, which is connected to the MHC locus on chromosome 6p21. Type 1 diabetes is tightly clustered in families. This association is supported by a recent study that looked at 1435 multiplex families.

Type 2

The pancreatic beta cells in people with type 2 diabetes are less able to release enough insulin to maintain normal glucose and lipid balance, which is why type 2 diabetes is a condition of relative insulin deficit. Insulin resistance is associated with age, obesity, and less physical activity than normal. The total genetic risk ratio for type 2 diabetes ranges from 2 to 4, which is lower than the risk ratio for type 1 diabetes. The genetic contribution to type 2 diabetes is lower than that of type 1. Genes that are important in type 2 diabetes have been found using genome-wide scanning, with the most promising results occurring on chromosomes 1q21-q24, 2q37, 12q24, and 20. Other linkage areas are now being investigated, and it is possible that in the future novel type 2 diabetes susceptibility genes may be discovered.

Both type 1 and type 2 diabetes are hereditary conditions, with type 2 diabetes having a far greater genetic influence. The hereditary risk ratio for type 1 is 15, whereas the risk ratio for type 2 is around 2. There is a possibility that the genes that contribute to type 1 diabetes are distinct from those that contribute to type 2 diabetes. It's possible that distinct groups of genes will define varying levels of risk for diabetes complications.

While doing research about this topic for personal reasons, I came across these two articles (links below) that I felt explained how diabetes types 1 and 2 can be linked to your genetics. In my opinion, the research being done currently on genes being connected to diabetes is crucial in order to understand the disease even more. There is a large percentage of people in the United States who have diabetes type 1 or type 2, so it is important to understand this disease as much as possible.

https://journals.lww.com/jasn/Fulltext/2006/02000/Genetics_of_Diabetes_and_Its_Complications.10.aspx

https://www.sciencedirect.com/science/article/pii/S0303720713001408?casa_token=JilclpDEi58AAAAA:Ggc7VCavwYnGASBXyJhrPoLzAzwy1PV0X0XCfPetUWCxcuVGdk6w-bJorniMS4sgDRyAo0HD-9_V

Fighting Genetic Diseases with Moths and Magnets

 

There are endless genetic diseases, such as cystic fibrosis, muscular dystrophy or even spinal muscular atrophy, where a cure is yet to be found. However, Gang Bao and his team of bioengineers at Rice University have developed a potential new gene therapy for these incurable genetic disease by utilizing moths and magnets. This new technology combines a virus that infects the North American moth, Autographa californica, and nanoparticles to potentially repair the mutations that cause genetic diseases. The moth infecting virus is crucial in this experimental research for it serves as a carrier for CRISPR/Cas9, which is an system consisting of an enzyme and piece of RNA that is often used as a genome editing tool. The magnetic field works to manipulate gene expression of the virus, which is normally inactive in blood, in the targeted tissues. Nevertheless, the main challenge to their work was finding a process in which CRISPR/Cas9 can be delivered to the target area with high efficiency. When working to solve this roadblock, the team had to ensure that only the target area was affected because altering the DNA of other tissues or organs could be detrimental.

    Bao’s group developed a way around this problem by specifically choosing the moth-infecting virus. This virus contains cylindrical baculovirus vector (BV), which is the part of the virus that acts as a unit to carry the CRISPR/Cas9. The BV is able to transport the CRISPR/Cas9 to the target site since there naturally exists a protein (C3) which inactivates the BV. Once the BV reaches the site of interest, a magnetic field is applied and is then able to overcome the deactivation caused by C3. Thus, the CRISPR/Cas9 can then serve its purpose of repairing the mutations that give rise to the genetic diseases.

   I feel as if this work is important to the scientific community’s understanding of incurable diseases even if it does not end up being the be all end all answer to stopping the diseases entirely. This work will definitely contribute in enhancing gene therapies and at least reduce the side effects of the disease while making life on those facing these challenges easier. Personally, the most interesting aspect of article was that during the testing process the team had used Green Fluorescent Proteins (GFP) to determine if the use of magnets contributed to increasing delivery efficiency of BV to the target site. Since students have been working with GFP in the laboratory, it was a nice to see how work done within the weekly labs can be related to groundbreaking work done out in the field.

Resources:

https://www.sciencedaily.com/releases/2018/11/181113110359.htm

Concerns Arise about CRISPR Safety and Genome Vandalism

Media has a way of portraying science fiction and scientific technologies in an outrageous way, like changing humans into creatures through the use of CRISPR (clustered regularly interspaced short palindromic repeats) technology. CRISPR was seen in bacterial defense and was used to destroy DNA that entered the bacteria, but is now used to edit and alter specific DNA sequences. In humans, though, CRISPR can ultimately be used to treat improve health, improve food, treat cancers and diseases and potentially suppress the effect of environmental pollution.

How CRISPR works.

However, concerns are arising on the problems with CRISPR. Some research suggests that the use of CRISPR at a specific sequence can damage DNA further along the chromosome, and this makes some caution to be needed when using CRISPR in clinical settings.

In humans, some trials have been planned to help treat human diseases. Two main trials have been planned in order to treat blood diseases (beta-thalassemia and sickle cell anemia). The trials use gene editing outside of the patient’s body (ex vivo). The thought is that researchers will take hematopoietic blood cells and edit them and “correct” them. Once the genes are corrected and the cells are normal, they will be reintroduced into the patient’s body to cure the disease. This theory has been used in China to test treatments on human cancers. Using immune T cells, researchers use CRISPR to stop the cells from producing a PD-1 protein, and allows T cells to now attack cancer cells.

Although in theory these treatments seem flawless, there are some concerns. Some studies suggest that using CRISPR may not be as effective as thought and have some side effects. One study says that when Cas9 cuts the DNA, it can potentially cause it to not be able to edit the DNA anymore. A bigger concern is about human exposure to CRISPR. Since CRISPR is a protein found in bacteria, many individuals may have already been exposed to it from bacterial infections, which causes the body to develop an immune response to the protein and therefore are unable to benefit from the CRISPR therapies. The last concern is that CRISPR is not totally accurate and may have the potential to cut the wrong DNA sites and cause disease.

I think that CRISPR is a discovery that changed genetics and clinical methods of treatment for diseases. Although it may have its impurities and potential dangers, I think that the CRISPR methods are one of the best out there as of now. There is inadequate research on the negative impacts of CRISPR after a long period of time. What if there are more implications for CRISPR after years? In addition, the use of CRISPR has ethical implications of potentially causing cancers and other diseases. Is it ethical to use CRISPR in humans when there is the potential of causing cancers and other diseases? Using the ex vivo method can help to identify the negatives before placing the cells back into the patient’s body, but there is still the possibility of cancers arising. Overall, I still think CRISPR is the best genetic engineering technique right now and the effects will not be truly known until it is used to treat human diseases more commonly. 

Rapamycin: The Cure

Genetic Diseases pose a problem in the human gene pool. Some may be a simple nuisance while others may be fatal. However, several scientists from the Okinawa Institute of Science and Technology Graduate University have used rapamycin to inhibit cell growth and division of mutated DNA. Within their study, about 45 mutated yeasts out of the 1000 studied were treated through rapamycin addition and in a way "cured". From such a treatment, they were able to identify 12 genes that can be treated with rapamycin. Adding rapamycin to these genes can cause the cells to function normally (divide and grow at a normal rate). 

Such a discovery is a step forward in the right direction. Treating genetic diseases would be a monumental undertaking, but with the scientists from Okinawa, the future looks brighter knowing that the possibility of treating genetic disorders can be done.


References:

Link to Article about Fission Yeast Genes

Link to Main Study

Transgenic skin received by Syrian refugee

A Syrian boy with a rare genetic disease has received an almost entirely new epidermal layer of skin from his own stem cells. This boy has a disease called Junctional epidermolysis bullosa  and has a mutated gene causing the basement membrane of the containing laminin 332 does not develop properly. so a group of scientists and pediatricians created Karatinocyte cultures from the boys stem cells , they used invivo and invitrio renewment of human epidermal cells, the boy will still have to live with the disease for the rest of his life and may also have issues with other systems in his body this disease is also known to affect the mucosa. besides the amazing accomplishment that this undergoing was, researchers were also able to end  a long standing discussion whether the epidermis was regenerated by many equally powerful progenitor cells or a fewer number of individual stem cells. The later of the two is true according to the researcher.

I believe any advancement in stem cell research is a good thing , the more we as a society can create new cells from a persons original cells is amazing and could help such a young child have anew lease on life from the cultivation of his own stem cells is remarkable.

Link 1

link 2

Gene Therapy Could Cure Congenital Eye Blindness

Recently scientists at the University of Oxford have developed a gene therapy treatment in the hopes of reversing the affects of congenital eye blindness. Congenital eye blindness is a genetic disease that effects 1 in every 50,000 people, most commonly  males. The disease is due to a single gene mutation that causes a gradual loss of light detecting retinal cells. Patients are born with full eye sight and find that their vision progressively narrows until they eventually become completely blind. As of yet there have been no successful treatments developed to slow the progression of this disease. However, there have been many attempts to develop treatment for a number of eye conditions. Diseases effecting the eye are often caused by only one or two genes and eyes can be easily accessed for administration of treatments, this makes eye conditions desirable for scientists to work on. 

The gene therapy treatment developed by the scientists at the University of Oxford is administered through an injection into the eye. The injection contains a virus administered directly into the retina. This virus contains billions of functioning copies of the defective gene. With this working copy the retinal cells can in turn function properly. This experimental treatment was administered to six patients. In wonderful news results from the study published in the New England Journal of Medicine on April 28, 2016 reported that the treatment had seen great success. After four years not only did the treatment slow progression of the disease, it reversed the effects in some cases. The youngest tested patient received the best results, leading scientists to the conclusion that early administration is best. However, all patients regardless of age saw astounding results. The success of this treatment has scientists hopeful in the successful treatment of other eye conditions. I am interested to see where this great success takes the treatments of genetic eye diseases, and how the study of this therapy on a larger population size results. 

First IVF Puppies

Scientists from Cornell University were able to successfully deliver a litter of puppies that were conceived through the process of in vitro fertilization. Scientists have been trying to accomplish successful in vitro fertilization in dogs since the 1970’s, but kept falling short. Scientist at Cornell University stated that the main challenges were “figuring out the optimal stage for fertilization of the female dog’s eggs and simulating the conditions in the lab for preparing sperm”. Eventually the team of scientists were able to transfer 19 embryos into a host female dog which gave birth to seven puppies. Five of the dogs were conceived from beagles and two were a mix of beagle and cocker spaniel. The embryos were cultivated in a dish in a laboratory before being implanted in the dog. The reason why this discovery is such a breakthrough is because scientists believe that the success of this experiment may help the future conservation of endangered species and may also help with gene-editing technologies that cure inherited diseases in dogs. Humans and dogs share more than 350 traits, and this breakthrough could help further the research of many genetic diseases.

I think that the success of this experiment is truly remarkable and that this will definitely be helpful when studying other genetic diseases in humans. I was surprised to learn that dogs and humans share over 350 traits. Hopefully in the future in vitro fertilization will be useful in the conservation of various endangered species.

Original Article

Gene Therapy is Now Treating Blood Disease

Hemophilia B, also called factor IX, is a genetic disorder in which factor IX is missing and prevent clotting of the blood. There is about a 0.02% chance of a live birth being affected by the disease in the United States. Each race is affected differently by the disease and different ethnicities show different frequencies of the disease affecting live births. There are vast efforts to hopefully cure the disease on day. In Britain six patients ailed with the disease were treated for it by being injected with the correct form of the defective gene. This is quite the achievement for gene therapy, especially since it began to carry a bad reputation after the early 2000's. Many doctors say that this break through could potentially bring the field of genetic therapy back into the modern medical industry.

The general concept of gene therapy consists of replacing defective genes in any genetic disease with the corrected genetic sequence. Although it sounds simple, carrying out this task is much more difficult that thought to be. The corrected gene will be placed into a virus, with the hope that the virus will inject cells and distribute the DNA. However, the immune system seems to be a little too successful with killing viruses.

With the advance that this injection of the corrected gene of factor IX has provided however, it has not only given insight on how to treat hemophilia B, but also how to possibly treat multiple other diseases in the future. This treatment has opened many doors to possibly being able to treat other genetic disorders. Also the way that this specific blood type was treated may be able to shed some light on the ability of eukaryotes to use corrected DNA sequences. A very close family friend of ours has hemophilia, and this cure if it comes to the United States could give her her life back by reducing the number of transfusions and medications she needs to take daily. I think that the cure for this type of hemophilia is ground breaking and can only further genetic technology in the medical field.

The original article can be found here.
The National Hemophilia Foundation's link can be found here.

mbPAINT and Genetic Diseases

    This month, ScienceDaily shared an article about DNA mapping. With high-tech optical tools, researchers of Rice University have now found a way to pinpoint the location of specific sequences along single strands of DNA. This technique has been proven to someday help diagnose genetic diseases. Chemist Christy Landes, a lead researcher, identified DNA sequences as short as 50 nucleotides at room temperature using a technique called super-localization microscopy. This would be impossible to see with a standard microscope because it cannot comprehend such small targets. Also, it cannot be done with electron microscopes because it requires the targets to be frozen. Super-localization microscopy has been known about for a while but is just now being used in biosensing. For a while now, scientists have been able to see double-stranded DNA molecules, but Landes says the ability to see single-stranded DNA is a new victory in science. Landes and her researchers call their technique the "motion blur point accumulation for imaging in nanoscale topography," or mbPAINT. This technique has allowed them to resolve structures as small as 30 nanometers by creating a movie-like drift of fluorescent DNA probes flowing over a known target sequence along an immobilized single strand of DNA.



    To create effect, the probes were labeled with a fluorescent dye that lights up only when attached to the target DNA. Normally, they would flow unseen, but a few would bind to the target just long enough to be captured by the camera before they were pulled away by the moving liquid. The processing of these images will allow researchers to image extremely small objects, smaller than the natural diffraction limit of light-based imaging. To the naked eye, in real time you would only see a line due to the rapid speed of the probes. This technology allows researchers to see biological processes of nano-sized objects. It shows as they happen in water, with salts, at room temperature and even in a cell. So, what is planned for the future? Landes hopes to be able to someday map even smaller fragments of DNA. Instead of seeing 50 nucleotides, she hopes to be able to look at only a few. Landes stated, "Some diseases are characterized by one amino acid mutation, which is three nucleotides, and there are many diseases associated with very small genetic mutations..." With this being said being able to get it down to just a couple nucleotides could become extremely helpful with genetic disease study.

In my opinion I feel that this new development in DNA strand study can become extremely beneficial to not only the field of science, but also human health. For many years researchers have been studying genetic diseases but can only go so far. Super-localization microscopy has now offered many people hope to finding specific mutation in genetic diseases that have not yet been identified. If Landes and her researchers were able to identify DNA sequences as short as 3 nucleotides, it would be an amazing scientific find, especially considering a great amount of genetic diseases have small, localized mutations. In addition, the mbPAINT method is very cost-effective.

Article: http://www.sciencedaily.com/releases/2013/10/131009111151.htm

Link: This is a video of what it looks like to see the single-strand  localization http://www.youtube.com/watch?v=dc6i3ZkZhd0&list=PL46869D7222684E1A

Fifty-Hour Whole Genome Sequencing Provides Rapid Diagnosis for Children With Genetic Disorders

At the Children’s Mercy Hospitals and Clinics in Kansas City, a report has been made that critically ill infants can be diagnosed using an entire genome sequence.  The impressive part about this STAT-Seq is that in about 50 hours a patient can have their whole genome sequenced to detect genetoc diseases. This is even more impressive in comparison to current testing that can take more than six weeks just for a single gene sequence.  The software that STAT-Seq uses is programmed to search for 3,500 different genetic diseases, and marks the first time gene sequencing could influence treatment of urgent care patients. As the article states: three percent of all children and 15 percent of childhood hospitalizations are due to genetic disease.  Currently, early treatment can prevent disabilities and life-threatening diseases in 70 of 500 treatable genetic diseases.



There is no comparison between STAT-Seq and the current methods of genome sequencing. The human genome contains as many as 30,000 genes. The current method can code a single gene in about six weeks, where as the STAT-Seq can code the whole genome in about 50 hours.  There are no words to describe the difference between the two methods of sequencing. The ability to detect genetic disorders early creates a multitude of opportunities to benefit the quality of life as a human being. Diseases such as infantile Pompe disease and Krabbe disease can be helped therapeutically from early detection. The unknowns of phenomenons such as Sudden Infant Death Syndrom (SIDS) could potentially be discovered, and prevented with technology like the STAT-Seq. With the convergence of technology and medicine, a shift in personalized medicine can be made. The potential of personalized medicine is limitless, as each disease calls for a different therapeutic approach. In current times, personalized medicine has began to make its mark in the treatment of cancer, as each case is unique.

 

Treating Huntington's Disease with XJB-5-131

The University of Utah publishes information regarding one of the most severe genetic diseases found in humans, Huntington’s Disease.  Huntington’s Disease is caused by a genetic mutation on chromosome 4.  The disease causes harm by destroying the brain’s basal ganglia.  It is believed that this is caused by oxidative damage to mitochondria.  This part of the brain controls important functions such as thinking and movement.  A recent article published in Science Daily highlighted the work being done by scientists at the Lawrence Berkeley National Laboratory.  The scientists have synthesized a new compound that alleviates the symptoms of Huntington’s Disease in mice.

[caption id="" align="aligncenter" width="280" caption="Chromosome 4"][/caption]

The compound being tested is an antioxidant called XJB-5-131.  It is believed that the compound is able to improve the health of mitochondria and prevent the degradation of neurons.  The Huntington’s mice that were given the compound behaved and looked like mice that did not have the disease.  The scientists tested the motor skills and grip strength of mice with Huntington’s disease after being given XJB-5-131.  Nearly all of the affected mice were able to pass these tests, and the Huntington’s mice that were not given the compound performed much more poorly in the tests.  The scientists also studied the mitochondria of the mice that were given XJB-5-131 and found that the compound lessened the oxidative damage on the mitochondria.  With the success of XJB-5-131, the scientists are testing if derivatives of the compound yield better results.

The results from this study may lead to a cure for Huntington’s Disease.  This is incredibly important because of the severity of the disease.  Huntington’s Disease typically begins in people aged 30 to 50.  Upon the onset of the disease, a person will only live for 10 to 20 more years.  A cure derived from XJB-5-131 may allow those affected with the disease to live much longer and healthier lives.  This would benefit both the people with the disease and those present in their lives.

 

Genetic Diversity in Indian Populations and Its Health Implications

 

Lalji Singh, PhD, Director of the Centre for Cellular and Molecular Biology at the Council of Scientific and Industrial Research (CSIR) in India,  has been undertaking a study on the evolution of human populations, focusing specifically on genetic diseases.  While a popular focus for many researchers,  specific data on the origin and frequencies of genetic diseases in India has been relatively sparse.  India has "one of the most genetically diverse populations in the world."  This diversity is represented by the anthropologically well-identified 4,635  populations that share little to no gene flow between them.  This is a result of the culutrual, social, and geographical boundaries that have bolstered the propensity of interbreeding within individual populations.  Taking 132 samples from 25 of these major populations, each group representing a major piece of Indian life, location, and culture,  Singh analyzed and determined that there were originally two gentically independent divergent populations.  Having the most similar genetic composition to the Middle Easterners, Central Asians, and Europeans are the Ancestral Northern Indians while the other major group, the Ancestral Southern Indians, have a genetic affinity that aligns solely with the populations currently within the region.