Microsoft Excel forces human genes to be renamed / Humans + Tech - #41

+ A blood test that can detect cancer years before + Gene editing brain cells to curb the opioid epidemic + A brain hack that improves language learning + Using the wrong cells to study Covid-19

Hi,

I hope you had a good week. This is a medical focussed newsletter as most of the interesting articles I discovered this week were somehow from the medical field :)

Here we go:

Scientists rename human genes to stop Microsoft Excel from misreading them as dates

Anyone who uses Excel to import data knows that Excel will automatically format the data and often gets it wrong. For geneticists, this has proved to be a huge headache as genes named MARCH1 and SEPT1 are automatically converted to dates by Excel [The Verge].

Even if one scientist is aware of the issue and fixes it, other scientists may not, and eventually, the data gets polluted with errors. Excel is a wide-spread tool used in science, and the repercussions could be serious.

This is extremely frustrating, even dangerous, corrupting data that scientists have to sort through by hand to restore. It’s also surprisingly widespread and affects even peer-reviewed scientific work. One study from 2016 examined genetic data shared alongside 3,597 published papers and found that roughly one-fifth had been affected by Excel errors.

The HUGO Gene Nomenclature Committee (HGNC), finally decided that it’s easier to change the names of the genes than to wait for Excel to fix the issues.

Help has arrived, though, in the form of the scientific body in charge of standardizing the names of genes, the HUGO Gene Nomenclature Committee, or HGNC. This week, the HGNC published new guidelines for gene naming, including for “symbols that affect data handling and retrieval.” From now on, they say, human genes and the proteins they expressed will be named with one eye on Excel’s auto-formatting. That means the symbol MARCH1 has now become MARCHF1, while SEPT1 has become SEPTIN1, and so on. A record of old symbols and names will be stored by HGNC to avoid confusion in the future.

Being a frequent user of the Excel data import feature, I know how difficult and frustrating it is to resolve all the auto-formatting issues each time. I’m happy for all the genetic scientists that this is one less thing they have to worry about.


A blood test that can detect cancer years before symptoms appear

A team based in China has demonstrated the detection of five types of cancers, through a non-invasive blood test, years before symptoms start to appear [The Guardian].

“We demonstrated that five types of cancer can be detected through a DNA methylation-based blood test up to four years before conventional diagnosis,” the team wrote in the journal Nature Communications

They said the test was unlikely to be predicting cancer but rather picking up on cancerous growths that had not yet caused symptoms or been spotted by other methods.

[…]

The researchers reported how the new test was based on screening particular regions of DNA found in blood plasma for telltale tags, called methyl groups, that often crop up in tumour DNA. The team said they used techniques that allowed them to pick up even very small levels of such DNA.

They then used machine learning algorithms – a type of artificial intelligence – to develop a system that could determine whether any DNA found circulating in the blood was indeed shed by tumours, based on the presence of these methyl groups.

If validated in larger studies, this could be a boon to those who are potentially at risk. They can start treatments or therapies as early as possible, to delay the onset of cancer or to completely destroy it.


How gene editing a person’s brain cells could be used to curb the opioid epidemic

Craig W. Stevens, a Professor of Pharmacology at Oklahoma State University has proposed combining CRISPR gene-editing technology with a neurosurgical microinjection technique to treat patients using opioids to prevent them from overdosing [The Conversation].

Opioids kill by stopping a person from breathing. Respiratory nerves that contain opioid receptors are found in the lower part of the brain. When opioids bind to these receptors, they reduce the activity in the neurons and slow breathing. In the case of an overdose, breathing stops completely and the patient dies.

The treatment that Stevens proposes will use CRISPR to knock out the opioid receptor in the respiratory neurons. To locate the respiratory neurons, they will use an intracranial microinjection instrument.

Enter the intracranial microinjection instrument (IMI) developed by Miles Cunningham and his colleagues at Harvard. The IMI allows for computer-controlled delivery of small volumes of solution at specific places in the brain by using an extremely thin tube – about twice the diameter of a human hair – that can enter the brain at the base of the skull and thread through brain tissue without damage. 

[…]

Because the brain itself feels no pain, the procedure could be done in a conscious patient using only local anesthetics to numb the skin. Respiratory neurons drive the breathing muscles by firing action potentials which are measured by the recording wire in the tube. When the activity of the respiratory neurons matches the breathing movements by the patients, the proper location of the tube is confirmed and the CRISPR solution injected.

It’s an interesting technology that can potentially prevent thousands of deaths every year. I’m still very wary about gene-editing technology. I don’t think we know enough about the long-term effects of using it, but humans are always going to satisfy their curiosity. So let’s hope for the best and that it proves to be a net positive.


A brain hack that improves language learning abilities by 13%

Scientists from the University of Pittsburg's Sound Lab have discovered that small, imperceptible brain stimulation through the ear can result in a 13% improvement in the ability of adults to recognize foreign language tones [Inverse].

In the study, published Thursday in the journal Science of Learning, the authors explain that part of what has made language acquisition in later life difficult is that the adult brain no longer has the same plasticity — or ability to reshape its synaptic networks to accommodate new information — that it once did in childhood.

"Humans are excellent perceptual learners," the study team writes. "Yet, a notable and well-documented exception is the acquisition of non-native speech categories in adulthood."

However, recent research has found that stimulation to the nervous system paired with behavioral stimuli can result in improved plasticity and memory recall. To test this for language learning, the team designed a small, outer-ear device to non-invasively stimulate a participant's transcutaneous vagus nerve (tVNS) through painless electric pulses.

I found it hard to learn languages even in childhood, so I’m all for technologies that can help me learn languages easier. However, I think I’ll wait until we know if there are any side-effects to zapping the brain like this.


Scientists may be using the wrong cells to study Covid-19

One of the biggest pieces of misinformation in this pandemic has been the use of hydroxychloroquine to treat the coronavirus. To be clear, hydroxychloroquine doesn’t work as a treatment for Covid-19. And the whole debacle is because scientists have been basing their studies on the wrong type of cells [WIRED]. The culprit is kidney cells, also known as Vero cells from an African green monkey that died in 1962.

The ones derived from an African green monkey kidney, known as Vero cells, are especially popular among virologists, in part because they contain fewer antiviral proteins known as interferons than other cells, and thus provide a fertile breeding ground for certain viruses that are otherwise quite fickle and difficult to grow in the lab.

Vero cells have at times been indispensable to the study of coronaviruses. One of the earliest papers to identify the pathogen behind the 2003 SARS outbreak, for instance, used this kind of cell to grow the virus so that scientists could study it in detail. But the cells’ more recent use provides a cautionary tale. Whereas hydroxychloroquine does appear to stop SARS-CoV-2 from infecting Vero cells, it fails to do the same for human lung cells in a dish. According to research from Stefan Pöhlmann, head of the Infection Biology Unit at the German Primate Center in Göttingen, and his collaborators, the devil was in the details of how the cells interact with the SARS-CoV-2’s dreaded ‘spike’ protein. Human lung cells contain at least two different enzymes that can help the virus sneak through their membranes. With Vero cells, however, only one of those modes of entry is available—and it turns out to be the one that hydroxychloroquine will block. Pöhlmann and his team published the results in the journal Nature on July 22. For him, it’s a clear example of why using human lung cells is really important in studying this pandemic virus. Vero cells should be “handled with caution,” Pöhlmann says. “It’s true that the Vero cells are very popular. But unfortunately for this particular aspect of Covid-19 research, they are absolutely not useful. I think this is now clear to the field.”

One of the other problems around research conducted in this pandemic is that many scientists have abandoned their main areas of expertise to focus on Covid-19 and are not aware of the nuances of virology. This is even the case with virologists who have never with coronaviruses before and have now switched to working on Covid-19.

Madhu Pai, epidemiologist and director of the Global Health Program and TB Centre at McGill University in Montreal, has described this as the “Covidization of research,” where “well-intentioned scientists with real expertise in one field intrude into another, passing judgment where they lack expert-level training and insight.” The result, he says, is to “open the door to big mistakes with bad consequences.”


Quote of the week

Humanity has endured many crises over centuries. The COVID-19 crisis will also pass. The appeal of a quick fix or sudden influx of funding can be mesmerizing, but is it coming at the expense of moving forward other critical areas of health research? We need a long-term vision and strategy for research and scholarship. Short-term, crisis-driven thinking is neither strategic nor sustainable.

—Madukar Pai, Covidization of research: what are the risks? [Nature Medicine]

I wish you a brilliant day ahead :)

Neeraj