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More than skin deep: A molecular look at the mechanisms behind pigmentation variation

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More than skin deep: A molecular look at the mechanisms behind pigmentation variation


Researchers from the University of Pennsylvania have discovered key insights into the molecular basis of skin color variations among African populations. Their findings, published in Nature Genetics, broaden the understanding of human evolution and the genetics underpinning contemporary human skin color diversity.

“Despite the abundant genetic diversity within African populations, they have been historically underrepresented in genetic studies,” says senior author Sarah Tishkoff, a Penn Integrates Knowledge University Professor with appointments in the Perelman School of Medicine and School of Arts & Sciences. “Our findings offer novel information about the genetic basis and evolutionary history of skin color diversity, contributing to a clearer depiction of human evolution.”

The story of human evolution is as rich and diverse as the adaptations found across the world’s populations, Tishkoff says. She notes that, among many adaptive traits, skin color stands out as one of the most well-known. Darker skin tones, prevalent in equatorial regions, serve as nature’s very own sunblock, evolving over millennia to shield these populations from the sun’s intense ultraviolet radiation. Conversely, lighter pigmentation, as seen in populations closer to the poles, is an adaptation to mitigate the risks of insufficient sun exposure by maximizing vitamin D production, which is triggered by UV exposure.

“Our approach involved genome-wide association studies of skin color from more than 1,500 eastern and southern African individuals as well as scanning the genome to identify genetic variants that are highly differentiated between lightly-pigmented Khoesan-speaking San population and other darkly pigmented Africans and may play a role in local adaptation in that population,” says Yuanqing Feng, first author of the paper and a postdoctoral researcher in the Tishkoff Lab.

The researchers note that pigmentation is a complex trait influenced by hundreds of variants scattered across the genome, with the majority situated in noncoding regions. These noncoding variants may affect the expression of genes located up to one million bases away. The vast number of mutations associated with skin color and the uncertainty surrounding the target genes regulated by these mutations make it particularly arduous for researchers to find the precise genetic mechanisms governing this trait.

Feng and collaborators used massively parallel reporter assays to discern the regulatory activities of thousands of variants. This high-throughput technique narrowed down the thousands of candidates to 165 functional variants. To identify the target genes of these functional variants, Feng further constructed high-resolution chromatin interaction maps in melanocytic cells using chromatin conformation capture assays. “This is a high-resolution 3D genome map in melanoma cells that will be valuable for gene regulation studies in pigmentation and melanoma biology,” Feng says.

Using CRISPR/Cas9-based genome editing, the researchers discovered that mutations in an enhancer of OCA2, a gene associated with albinism, could lead to a 75% reduction in melanin levels when compared to control cells. Within the same OCA2 enhancer, the researchers identified two closely located regulatory variants, estimated to be 1.2 million years old and 57 thousand years old, with the latter coinciding with the period of human migration from Africa.

“This case illustrates the continuous evolution of human skin color, and it’s remarkable to observe the significant effects on skin pigmentation attributed to a single enhancer,” Feng says.

San people have relatively lighter pigmentation compared to other African populations and possess the oldest genetic lineages in humans. While it is hypothesized that the light skin color of the San may result from adaptation to a southern African environment, the genetic underpinnings of this adaptation remain elusive. The researchers pinpointed several crucial regulatory variants near MITF, LEF1, and TRPS1 that contribute to the skin color adaptation observed in the San.

“MITF, LEF1, and TRPS1 are involved in signaling pathways regulating both melanocyte differentiation and hair development,” Tishkoff says. “This suggests that the variants influencing the lighter skin pigmentation observed in the San people may also contribute to their distinctive hair morphology.” Notably, the variant near TRPS1 associated with lighter skin color is at nearly 100% frequency in the San and in most non-Africans, whereas the variant associated with darker skin color is common in most other African populations and in the darkly pigmented Melanesian population, a striking example of global adaptations to UV exposure.”

Additionally, the researchers found a novel gene impacting human skin pigmentation, CYB561A3, which regulates iron homeostasis and influences melanin levels in melanocytic cells. “To our knowledge, the role of CYB561A3 in skin pigmentation has not been reported before. Intriguingly, there have been reports linking intravenous iron infusion to skin hyperpigmentation. Given that CYB561A3 encodes an iron reductase, I am curious about the role of this protein in this process,” Tishkoff says.

“Our findings underscore the complexity of genetic factors influencing skin color and the benefits of including ethnically diverse and underrepresented populations in genetic studies,” she says. “Conducting functional studies on the impact of noncoding variants will enhance our comprehension of the genetics underlying complex human traits and disease risk.”

“The populations included in this study are from remote regions of Africa and required the use of a mobile lab set up in the field sites,” Tishkoff says. “The collaboration with our partners in Africa was key to the success of this research project.”

In future research, the Tishkoff lab would like to use its innovative functional genomics approach to identify more genetic variants contributing to human pigmentation and other adaptive traits in a larger sample of ethnically diverse Africans.

Sarah Tishkoff is the David and Lyn Silfen University Professor in Genetics and Biology and a Penn Integrates Knowledge University Professor with appointments in the Perelman School of Medicine’s Department of Genetics and Department of Medicine and in the School of Arts & Sciences’ Department of Biology at the University of Pennsylvania.

Yuanqing Feng is a postdoctoral fellow in the Tishkoff lab at Penn.

Other authors include Ning Xie, Chao Zhang, Fang Zhang, and Matthew E.B. Hansen of Penn; Fumitaka Inoue of Kyoto University; Shaohua Fan of Fudan University; Thomas Nyambo of Hubert Kairuki Memorial University; Sununguko Wata Mpoloka and Gaonyadiwe George Mokone of the University of Botswana; Charles Fokunang and Alfred K. Njamnshi of the University of Yaoundé; Gurja Belay of Addis Ababa University; Michael S. Marks of the Children’s Hospital of Philadelphia Research Institute; Elena Oancea of Brown University; and Nadav Ahituv of the University of California, San Francisco.

This research was supported by the National Institutes of Health (grants R35GM134957-01, 3UM1HG009408-02S1, 1R01GM113657-01, 5R01AR076241-02, and 1S10OD010786-01) and the Penn Skin Biology and Disease Resource-based Center (Grant NIH P30-AR069589).



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New drug shows promise in clearing HIV from brain

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More than skin deep: A molecular look at the mechanisms behind pigmentation variation


An experimental drug originally developed to treat cancer may help clear HIV from infected cells in the brain, according to a new Tulane University study.

For the first time, researchers at Tulane National Primate Research Center found that a cancer drug significantly reduced levels of SIV, the nonhuman primate equivalent of HIV, in the brain by targeting and depleting certain immune cells that harbor the virus.

Published in the journal Brain, this discovery marks a significant step toward eliminating HIV from hard-to-reach reservoirs where the virus evades otherwise effective treatment.

“This research is an important step in tackling brain-related issues caused by HIV, which still affect people even when they are on effective HIV medication,” said lead study author Woong-Ki Kim, PhD, associate director for research at Tulane National Primate Research Center. “By specifically targeting the infected cells in the brain, we may be able to clear the virus from these hidden areas, which has been a major challenge in HIV treatment.”

Antiretroviral therapy (ART) is an essential component of successful HIV treatment, maintaining the virus at undetectable levels in the blood and transforming HIV from a terminal illness into a manageable condition. However, ART does not completely eradicate HIV, necessitating lifelong treatment. The virus persists in “viral reservoirs” in the brain, liver, and lymph nodes, where it remains out of reach of ART.

The brain has been a particularly challenging area for treatment due to the blood-brain barrier — a protective membrane that shields it from harmful substances but also blocks treatments, allowing the virus to persist. In addition, cells in the brain known as macrophages are extremely long-lived, making them difficult to eradicate once they become infected.

Infection of macrophages is thought to contribute to neurocognitive dysfunction, experienced by nearly half of those living with HIV. Eradicating the virus from the brain is critical for comprehensive HIV treatment and could significantly improve the quality of life for those with HIV-related neurocognitive problems.

Researchers focused on macrophages, a type of white blood cell that harbors HIV in the brain. By using a small molecule inhibitor to block a receptor that increases in HIV-infected macrophages, the team successfully reduced the viral load in the brain. This approach essentially cleared the virus from brain tissue, providing a potential new treatment avenue for HIV.

The small molecule inhibitor used, BLZ945, has previously been studied for therapeutic use in amyotrophic lateral sclerosis (ALS) and brain cancer, but never before in the context of clearing HIV from the brain.

The study, which took place at the Tulane National Primate Research Center, utilized three groups to model human HIV infection and treatment: an untreated control group, and two groups treated with either a low or high dose of the small molecule inhibitor for 30 days. The high-dose treatment lead to a notable reduction in cells expressing HIV receptor sites, as well as a 95-99% decrease in viral DNA loads in the brain .

In addition to reducing viral loads, the treatment did not significantly impact microglia, the brain’s resident immune cells, which are essential for maintaining a healthy neuroimmune environment. It also did not show signs of liver toxicity at the doses tested.

The next step for the research team is to test this therapy in conjunction with ART to assess its efficacy in a combined treatment approach. This could pave the way for more comprehensive strategies to eradicate HIV from the body entirely.

This research was funded by the National Institutes of Health, including grants from the National Institute of Mental Health and the National Institute of Neurological Disorders and Stroke, and was supported with resources from the Tulane National Primate Research Center base grant of the National Institutes of Health, P51 OD011104.



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Chemical analyses find hidden elements from renaissance astronomer Tycho Brahe’s alchemy laboratory

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More than skin deep: A molecular look at the mechanisms behind pigmentation variation


In the Middle Ages, alchemists were notoriously secretive and didn’t share their knowledge with others. Danish Tycho Brahe was no exception. Consequently, we don’t know precisely what he did in the alchemical laboratory located beneath his combined residence and observatory, Uraniborg, on the now Swedish island of Ven.

Only a few of his alchemical recipes have survived, and today, there are very few remnants of his laboratory. Uraniborg was demolished after his death in 1601, and the building materials were scattered for reuse.

However, during an excavation in 1988-1990, some pottery and glass shards were found in Uraniborg’s old garden. These shards were believed to originate from the basement’s alchemical laboratory. Five of these shards — four glass and one ceramic — have now undergone chemical analyses to determine which elements the original glass and ceramic containers came into contact with.

The chemical analyses were conducted by Professor Emeritus and expert in archaeometry, Kaare Lund Rasmussen from the Department of Physics, Chemistry, and Pharmacy, University of Southern Denmark. Senior researcher and museum curator Poul Grinder-Hansen from the National Museum of Denmark oversaw the insertion of the analyses into historical context.

Enriched levels of trace elements were found on four of them, while one glass shard showed no specific enrichments. The study has been published in the journal Heritage Science.

“Most intriguing are the elements found in higher concentrations than expected — indicating enrichment and providing insight into the substances used in Tycho Brahe’s alchemical laboratory,” said Kaare Lund Rasmussen.

The enriched elements are nickel, copper, zinc, tin, antimony, tungsten, gold, mercury, and lead, and they have been found on either the inside or outside of the shards.

Most of them are not surprising for an alchemist’s laboratory. Gold and mercury were — at least among the upper echelons of society — commonly known and used against a wide range of diseases.

“But tungsten is very mysterious. Tungsten had not even been described at that time, so what should we infer from its presence on a shard from Tycho Brahe’s alchemy workshop?,” said Kaare Lund Rasmussen.

Tungsten was first described and produced in pure form more than 180 years later by the Swedish chemist Carl Wilhelm Scheele. Tungsten occurs naturally in certain minerals, and perhaps the element found its way to Tycho Brahe’s laboratory through one of these minerals. In the laboratory, the mineral might have undergone some processing that separated the tungsten, without Tycho Brahe ever realizing it.

However, there is also another possibility that Professor Kaare Lund Rasmussen emphasizes has no evidence whatsoever — but which could be plausible.

Already in the first half of the 1500s, the German mineralogist Georgius Agricola described something strange in tin ore from Saxony, which caused problems when he tried to smelt tin. Agricola called this strange substance in the tin ore “Wolfram” (German for Wolf’s froth, later renamed to tungsten in English).

“Maybe Tycho Brahe had heard about this and thus knew of tungsten’s existence. But this is not something we know or can say based on the analyses I have done. It is merely a possible theoretical explanation for why we find tungsten in the samples,” said Kaare Lund Rasmussen.

Tycho Brahe belonged to the branch of alchemists who, inspired by the German physician Paracelsus, tried to develop medicine for various diseases of the time: plague, syphilis, leprosy, fever, stomach aches, etc. But he distanced himself from the branch that tried to create gold from less valuable minerals and metals.

In line with the other medical alchemists of the time, he kept his recipes close to his chest and shared them only with a few selected individuals, such as his patron, Emperor Rudolph II, who allegedly received Tycho Brahe’s prescriptions for plague medicine.

We know that Tycho Brahe’s plague medicine was complicated to produce. It contained theriac, which was one of the standard remedies for almost everything at the time and could have up to 60 ingredients, including snake flesh and opium. It also contained copper or iron vitriol (sulphates), various oils, and herbs.

After various filtrations and distillations, the first of Brahe’s three recipes against plague was obtained. This could be made even more potent by adding tinctures of, for example, coral, sapphires, hyacinths, or potable gold.

“It may seem strange that Tycho Brahe was involved in both astronomy and alchemy, but when one understands his worldview, it makes sense. He believed that there were obvious connections between the heavenly bodies, earthly substances, and the body’s organs. Thus, the Sun, gold, and the heart were connected, and the same applied to the Moon, silver, and the brain; Jupiter, tin, and the liver; Venus, copper, and the kidneys; Saturn, lead, and the spleen; Mars, iron, and the gallbladder; and Mercury, mercury, and the lungs. Minerals and gemstones could also be linked to this system, so emeralds, for example, belonged to Mercury,” explained Poul Grinder-Hansen.

Kaare Lund Rasmussen has previously analyzed hair and bones from Tycho Brahe and found, among other elements, gold. This could indicate that Tycho Brahe himself had taken medicine that contained potable gold.



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Nitrogen emissions have a net cooling effect: But researchers warn against a climate solution

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More than skin deep: A molecular look at the mechanisms behind pigmentation variation


An international team of researchers has found that nitrogen emissions from fertilisers and fossil fuels have a net cooling effect on the climate. But they warn increasing atmospheric nitrogen has further damaging effects on the environment, calling for an urgent reduction in greenhouse gas emissions to halt global warming.

Published today in Nature, the paper found that reactive nitrogen released in the environment through human activities cools the climate by minus 0.34 watts per square metre. While global warming would have advanced further without the input of human-generated nitrogen, the amount would not offset the level of greenhouse gasses heating the atmosphere.

The paper was led by the Max Planck Institute in Germany and included authors from the University of Sydney. It comes one day after new data from the European Union’s Copernicus Climate Change Service indicated that Sunday, 21 July was the hottest day recorded in recent history.

The net cooling effect occurs in four ways:

  • Short-lived nitrogen oxides produced by the combustion of fossil fuels pollute the atmosphere by forming fine suspended particles which shield sunlight, in turn cooling the climate;

  • ammonia (a nitrogen and hydrogen-based compound) released into the atmosphere from the application of manure and artificial fertilisers has a similar effect;

  • nitrogen applied to crops allows plants to grow more abundantly, absorbing more CO2 from the atmosphere, enabling a cooling effect;

  • nitrogen oxides also play a role in the breakdown of atmospheric methane, a potent greenhouse gas.

The researchers warned that increasing atmospheric nitrogen was not a solution for combatting climate change.

“Nitrogen fertilisers pollute water and nitrogen oxides from fossil fuels pollute the air. Therefore, increasing rates of nitrogen in the atmosphere to combat climate change is not an acceptable compromise, nor is it a solution,” said Professor Federico Maggi from the University of Sydney’s School of Civil Engineering.

Sönke Zaehle from the Max Planck Institute said: “This may sound like good news, but you have to bear in mind that nitrogen emissions have many harmful effects, for example on health, biodiversity and the ozone layer. The current findings, therefore, are no reason to gloss over the harmful effects, let alone see additional nitrogen input as a means of combatting global warming.”

Elemental nitrogen, which makes up around 78 percent of the air, is climate-neutral, but other reactive nitrogen compounds can have direct or indirect effects on the global climate — sometimes warming and at other times cooling. Nitrous oxide (N2O) is an almost 300 times more potent greenhouse gas than CO2. Other forms of nitrogen stimulate the formation of ozone in the troposphere, which is a potent greenhouse gas and enhances global warming.

Professor Maggi said the research was important as it helped the team gain an understanding of the net-effect of the distribution of nitrogen emissions from agriculture.

“This work is an extraordinary example of how complex interactions at planetary scales cannot be captured with simplistic assessment tools. It shows the importance of developing mathematical models that can show the emergence of nonlinear — or unproportional — effects across soil, land, and atmosphere,” he said.

“Even if it appears counter-intuitive, reactive nitrogen introduced in the environment, mostly as agricultural fertilisers, can reduce total warming. However, this is minor compared with the reduction in greenhouse gas emissions required to keep the planet within safe and just operational boundaries.

“New generation computational tools are helping drive new learnings in climate change science, but understanding is not enough — we must act with great urgency to reduce greenhouse gas emissions.”

Gaining a holistic understanding of the impacts of nitrogen

The scientists determined the overall impact of nitrogen from human sources by first analysing the quantities of the various nitrogen compounds that end up in soil, water and air.

They then fed this data into models that depict the global nitrogen cycle and the effects on the carbon cycle, for example the stimulation of plant growth and ultimately the CO2 and methane content of the atmosphere. From the results of these simulations, they used another atmospheric chemistry model to calculate the effect of man-made nitrogen emissions on radiative forcing, that is the radiant energy that hits one square metre of the Earth’s surface per unit of time.



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