Detecting Cancer Risk in Gene Variants Using CRISPR

 CRISPR technology has been used in many novel ways in modern genetic research through its ability to modify the DNA of living organisms. By utilizing two different gene editing methods, researchers at ETH Zurich have found a way to investigate how genetic mutations relate to cancer. Using CRISPR, the researchers modified the EGFR gene in two human cell lines in more than 50,000 different variations to create mutated cells which they tested. This was achieved by first modifying the base pair sequence in the genes using base editing, which allows for the replacement of cytosine with thymine and adenine with guanine. Prime editing, a less reliable technique that can swap any DNA base, was then used afterwards to finish the base pair replacement. 

The researchers found that there were ten formerly uncertain variants which now have evidence suggesting that they are significant to cancer, either in its onset or its resilience. They also found a mechanism by which the EGFR gene could cause cancer. Lastly, they found six new variants that have never been observed that could play a role in cancer.

The research described above has only scratched the surface of the potential this new method has. The variants in all other genes are now at researchers' disposal to be decoded and analyzed using this method, and could lead to further understanding in the fields of genetics and oncology as a whole. 

Diagram demonstrating how CRISPR technology modifies DNA.

https://www.sciencedaily.com/releases/2024/11/241112123149.htm

https://www.nature.com/articles/s41587-024-02439-1#Sec2

Genetics and Human Cranial Vault Shape: A Reevaluation

The human skull, a complex structure that protects the brain. The question lies on what genetic factor dictates cranial morphology? New shocking evidence was found by researchers at the University of Pittsburgh and KU Leuven that 30 regions of the genome are associated with the shape and structure of the brain. More importantly, 29 of these are new findings that weren't reported prior. Prior research of genes flourished results in rare human conditions. However, lack of awareness was shown on the genetic basis for typical features of the general public.  This awareness will produce enrich results. In addition, the following suggestions paleoanthropology studies, implementing different measures to describe vault shape, and variants in gene association. 
           Among the following suggestions, variants in gene association sheds light on the bigger picture. A discovery of the strong association near genes can dictate different results in formation of the head and skull. This relates to two variants near the gene RUNX2 that could coordinate development of the bone structure of the skull, or having global effects of the cranial vault. Another aspect is three variants BMP2, BBS9 and ZIC2 corresponding to Craniosynostosis. These variants suggest genes could aid in the development. 
        Overall, the human skull is a complex structure. It's clear that unlocking the human genome is a trip down the rabbit hole. As new technologies and methods immerse, more luck in understanding the secrets to be found within the genome that impact the cranial vault.

Links:

https://www.sciencedaily.com/releases/2023/11/231117120657.htm

https://www.nature.com/articles/s41467-023-43237-8#:~:text=The%20cranial%20vault%20in%20humans,genetic%20architecture%20remains%20poorly%20understood

Genetic Differences in Digestion Between Andean Populations

This study inspected the ancient genomes extracted from the Peruvian highlands with comparison more modern genomes from identical regions, that being highland and low-land regions, to identify genomic characterisitcs prevalent prior to the arrival of Europeans. The two regions have distinct environments making it suitable for study of how selective pressures can provoke adjustments in genomes, but is not limited to difference in altitude and agricultural practices. The lowlands were also more suspectable to the introduction of smallpox with the arrival of the Spanish as compared to the more remote Andean highlands.

The gene, MGAM, plays a role in the digestion of starch and has shown to demonstrate variants in the ancient genome that align with the start of potato domestication. A different configuration of MGAM was identified among the high-altitude population as compared to hunter-gatherer populations. The study potentially identified a variant of the DST gene. This gene modification is suggested to be correlated to enlarged right ventricles in individuals living in the highlands. This finding is in line with the suggestion of adaptation to high altitude among Andeans. 

It was found that the results differ from genomic changes among European populations as it relates to dietary changes, but with the rise in grain production in European regions. This was the increase in the amylase encoding gene, which serves as a starch digestive enzyme in saliva. Understand these differences in digestion could improving the treatment of diet related illness by acknowledging genetic differences among populations, such as their ability to digestion starchy foods, and which treatment would be ideal.

COVID-19 and Loss of Smell

Many individuals diagnosed with COVID-19 typically also suffer from the loss of taste or smell. According to an article, researchers have now pinpointed the genetic variants in humans suffering from losing different senses. A study was conducted with nearly 70,000 adults with COVID-19 and found that individuals with specific genetic mishaps on chromosome 4 were eleven percent more likely to lose the ability of their senses, whether taste or smell, than those individuals without the changes on their chromosome. The two genes, UGT2A1, and UGT2A2, help humans smell and happen to reside in the region of chromosome 4 that is linked to sensory loss during infection, found by Janie Shelton of 23andMe. Both of these genes make enzymes that metabolize substances called odorants, producing distinctive smells. 

For me, when I had covid, I lost my sense of smell, and I know a few other individuals and family members who have as well. I also do remember that news reports did suggest that one of the symptoms of COVID-19 is losing the sense of smell but I never heard of anyone loosing their sense of taste. When being sick many people loose their sense of taste especially if one has a sore throat. I believe more research may have to go into this study to se exactly how we loose our smell or taste for some individuals. 

New Mutations being created due to Coronavirus Variants

In an article from the New York Times, scientists writing a study have discovered that there are possibly new variants that are creating mutations that could possibly affect people more effectively and easily than the virus gene. The protein spikes latch onto human cells vigorously then moves on releasing their genes into the human body affecting close cells. The scientists involved in the research gathered positive coronavirus test results to try and factor out how the mutations are being created due to the variants. They also stated that the 677 mutations have altered the spike protein that is close to the spot where our proteins will nick the virus. 

Dr. Soumya Swaminathan, who is a chief scientist at World Health Organization (WHO), recently talked about the new variant that is N501Y mutation. This mutation has the same effects as the coronavirus, in terms of how it is transferred from one person to the next. The N501Y mutation was found in the UK and South Africa, and researchers have found that it spreads more quickly and is more infectious.

From reading both articles and gaining a better understanding of the coronavirus and the new variants being created and causing these mutations, I think the same way it is recommended to slow the spread of the virus is the same way we should be treating these new mutations. As Dr. Swaminathan said, we have to keep following the same guidelines that have been set out by the Center for Disease Control and Prevention (CDC) to keep these viruses at bay.

Genes underlying dogs' social ability revealed

Dogs were the first animal to be domesticated by humans, and it may have been as early as 16,000 years ago. In these thousands of years spent together, both species have co evolved and changed their relationship from what it started out as.  Dogs were first domesticated by early humans to serve as a wet nurse and help care for young babies while the parents were off hunting and gathering.  Since then, dogs have developed much better abilities to communicate and cooperate with humans.  Dogs often times come to humans for help, whereas their ancestral wolf would rather find solutions on its own.  A new study published in Scientific Reports searched for any relationship between this change in behavior and the genetic makeup of the dogs.

human and puppy bonding together

The study observed 500 beagles with previous experience around humans, and then presented the beagles with a problem. The problem was to open a sealed container that has food in it, and when they accepted it was too difficult, they observed if the beagles turned to human contact to solve the problem.  Of the 500 beagles studied, 200 of them were selected to have their DNA studied using a genome-wide association study (GWAS). The GWAS is able to find out if a particular gene variant is present in the dogs who exhibit a specific trait. A direct correlation was found using this method which determined that there actually were gene variants for the dogs who seeked human contact. Further support for this hypothesis would be if they performed this experiment on different dog breeds and still got similar results.

link to full article

Inherited gene changes take years off life expectancy

Researchers have linked a shorter lifespan with two common gene changes called variants. The researchers found these common variants near APOE and CHRNA3/5 genes to be associated with lifespan. One copy of either of these two changes to your DNA could shave a year off your life expectancy. People who inherit two copies, one from each parent of both variants could expect to lose about 3.3 to 3.7 years.

APOE gene has been linked to Alzheimer's dementia, high cholesterol, and coronary disease risk. The CHRNA3/5 gene is associated with an increased risk of lung cancer, nicotine dependence, and respiratory problems in smokers. Apparently These variants are pretty common in the population, as more than two-thirds of us will inherit a single copy of one of these DNA changes. And 3 in 1,000 people will inherit two copies of both variants. The variants have age and sex related effects on lifespan. The variant linked to Alzheimer's has a greater impact on older women, while the variation associated with lung disease influences middle-aged men more.



"Although the effect of these genetic variants on lifespan is surprisingly large, it is important to remember that this is only part of the story. Lifestyle has the greatest impact on how long we live and that is under our control." (Peter Joshi)

Original source: http://www.nature.com/ncomms/2016/160331/ncomms11174/full/ncomms11174.html
Related source: http://www.eurekalert.org/pub_releases/2016-03/uoe-igc033016.php

Good Memories Linked to Genes

         Have you ever found it difficult to recollect a certain memory, for example like a name of someone you just met? A new study indicates that there are specific genes that are linked to poor memory capabilities. Professor Ian Deary of the University of Edinburgh in the UK, along with many respectable colleagues that range from France to the US have conducted this experiment.

                                                 From: http://en.wikipedia.org/wiki/Apolipoprotein_E
     
          The researchers utilized five different studies based at the University previously mentioned. Because of the numerous colleagues involved, the researchers were able to analyze results from over 30000 people over the age of 45. The participants had to undergo a memory test. this memory test included short responses after reading a passage and also word memory questions. The results obtained showed that the lower scores the participants received on the memory test also had variants near the gene Apolipoprotein E and other kinds of genes. The researchers also mention that this gene comes with increased risk of Alzheimer's and Dementia. This could potentially be an early indicator to other response diseases.

         This articles was very interesting to me. If the gene could be assessed at an earlier age in people, the problems of Alzheimer's can be minimized. Memory is a very important process in the human body, further studies is needed.

Article: http://www.medicalnewstoday.com/articles/286106.php
Related Article: http://www.nature.com/nrneurol/journal/v9/n2/full/nrneurol.2012.263.html

Better Memory Performance linked to Genetic Variant

     The largest study to date of human memory using genomic data was done by the research team of IU School of Medicine, led by post-doctoral medical student Vijay K. Ramanan. This test included over 14,000 older adults. An analysis of genomic data using memory performance test was used to identify a specific location in the genome that was associated with better memory performance. According to an International research team, the results obtained can lead to finding new treatments for memory impairments (such as Alzheimer Disease).

                                        From: http://newsoffice.mit.edu/2013/discovering-hippocampal-connections

      This test involved chromosomal manipulation. There were higher performance tests of episodic memory that was associated with the DNA on chromosome 2; specifically the gene involved a G instead of the more common A nucleotide (in the gene called FASTKD2). The single genetic variant nucleotide polymorphism of SNP was found to also have a denser gray matter in the brain and a slightly larger hippocampus. These foundings were brought by Resonance Imaging Scans.

      This is a fantastic stepping stone for research on genetic variants. More research obviously needs to be done to determine whether the drug targeting the FASTKD2 gene can be used to protect against memory loss. But if these findings are verified, Alzheimer Disease can finally have a treatment associated with it.  

Article from: http://www.medicalnewstoday.com/releases/285378.php
Related article: http://www.ncbi.nlm.nih.gov/pubmed/19863254

Kids' genetic risk for obesity increases with age

Researchers at University College London have been studying genes and their role in childhood obesity. Their study  involved looking at different genetic variants in pairs of twins, ages four and ten. Body-mass index was also studied for kids of both ages. According to their research, the genetic variants rose over the years, growing from 43% in children of age 4 to 82% in children of age 10. These results show that "genetic predisposition to obesity is increasingly expressed throughout childhood," co-leader Clare Llewellyn states.This study brings hope that childhood obesity may be able to be reduced if intervention occurs at a young enough age. The link below lists some tips for overweight children, that will help with their weight-loss goals.
http://www.webmd.com/parenting/raising-fit-kids/move/kids-exercise-tips