Lab-grown ‘Mini-bile Ducts’ Used to Repair Human Livers in Regenerative Medicine first (Medicine)

For the first time, this new study has successfully created ‘mini-organs’ in the lab, that could help patients with liver damage

Scientists have used a technique to grow bile duct organoids – often referred to as ‘mini-organs’ – in the lab and shown that these can be used to repair damaged human livers. This is the first time that the technique has been used on human organs.

The research, from the University of Cambridge, Wellcome-MRC Cambridge Stem Cell Institute and the Wellcome Sanger Institute, paves the way for cell therapies to treat liver disease. In other words, growing ‘mini-bile ducts’ in the lab as replacement parts that can be used to restore a patient’s own liver to health – or to repair damaged organ donor livers, so that they can still be used for transplantation.

Bile ducts act as the liver’s waste disposal system, and malfunctioning bile ducts are behind a third of adult and 70 per cent of children’s liver transplantations, with no alternative treatments. There is currently a shortage of liver donors – according to the NHS, the average waiting time for a liver transplant in the UK is 135 days for adults and 73 days for children. This means that only a limited number of patients can benefit from this therapy.

Approaches to increase organ availability or provide an alternative to whole organ transplantation are urgently needed. Cell-based therapies could provide an advantageous alternative. However, the development of these new therapies is often impaired and delayed by the lack of an appropriate model to test their safety and efficacy in humans before embarking in clinical trials.

Now, in a study published today (18 February) in Science, scientists at the University of Cambridge, Wellcome-MRC Cambridge Stem Cell Institute and the Wellcome Sanger Institute have developed a new approach that takes advantage of a recent ‘perfusion system’ that can be used to maintain donated organs outside the body. Using this technology, they demonstrated for the first time that it is possible to transplant biliary cells grown in the lab known as cholangiocytes into damaged human livers to repair them. As proof-of-principle for their method, they repaired livers deemed unsuitable for transplantation due to bile duct damage. This approach could be applied to a diversity of organs and diseases to accelerate the clinical application of cell-based therapy.

“Given the chronic shortage of donor organs, it’s important to look at ways of repairing damaged organs, or even provide alternatives to organ transplantation. We’ve been using organoids for several years now to understand biology and disease or their regeneration capacity in small animals, but we have always hoped to be able to use them to repair human damaged tissue. Ours is the first study to show, in principle, that this should be possible.”

Dr Fotios Sampaziotis from the Wellcome-MRC Cambridge Stem Cell Institute

Bile duct diseases affect only certain ducts while sparing others. This is important because in disease, the ducts in need of repair are often fully destroyed and cholangiocytes may be harvested successfully only from spared ducts.

Using the techniques of single-cell RNA sequencing and organoid culture, the researchers discovered that, although duct cells differ, biliary cells from the gallbladder, which is usually spared by the disease, could be converted to the cells of the bile ducts usually destroyed in disease (intrahepatic ducts) and vice versa using a component of bile known as bile acid. This means that the patient’s own cells from disease-spared areas could be used to repair destroyed ducts.

To test this hypothesis, the researchers grew gallbladder cells as organoids in the lab. Organoids are clusters of cells that can grow and proliferate in culture, taking on a 3D structure that has the same tissue architecture, function and gene expression and genetic functions as the part of the organ being studied. They then grafted these gallbladder organoids into mice and found that they were indeed able to repair damaged ducts, opening up avenues for regenerative medicine applications in the context of diseases affecting the biliary system.

The team used the technique on human donor livers taking advantage of the perfusion system used by researchers based at Addenbrooke’s Hospital, part of Cambridge University Hospitals NHS Foundation. They injected the gallbladder organoids into the human liver and showed for the first time that the transplanted organoids repaired the organ’s ducts and restored their function. This study therefore that their cell-based therapy could be used to repair damaged livers.

“This is the first time that we’ve been able to show that a human liver can be enhanced or repaired using cells grown in the lab. We have further work to do to test the safety and viability of this approach, but hope we will be able to transfer this into the clinic in the coming years.”

Professor Ludovic Vallier, joint senior author from the Wellcome-MRC Cambridge Stem Cell Institute, and Honorary Faculty member at Wellcome Sanger Institute

Although the researchers anticipate this approach being used to repair a patient’s own liver, they believe it may also offer a potential way of repairing damaged donor livers, making them suitable for transplant.

“This is an important step towards allowing us to use organs previously deemed unsuitable for transplantation. In future, it could help reduce the pressure on the transplant waiting list.”

Mr Kourosh Saeb-Parsy from the Department of Surgery at the University of Cambridge, joint senior author

Funding

The research was supported by the European Research Council, the National Institute for Health Research and the Academy of Medical Sciences.


Reference

Sampaziotis, F et al. Cholangiocyte organoids can repair bile ducts after transplantation in human liver. Science 2021; 371: 839-846. DOI: 10.1126/science.aaz6964 https://science.sciencemag.org/content/371/6531/839


Provided by Wellcome Sanger Institute

Gene That Helps Control Egg’s Journey Sheds Light On Why Ectopic Pregnancy May Occur (Medicine)

Study details the first evidence of gene regulation in the transit of eggs from the ovaries to the uterus in mammals

Ectopic pregnancy is one of the most common prenatal complications, yet the cause of the condition remains unknown. Now researchers at the Wellcome Sanger Institute have pinpointed a gene in mice that plays a key role in the egg’s journey from the ovary to the uterus. When the gene Adgrd1 was deleted, female mice became infertile because the eggs remained stuck in the fallopian tubes.

The study, published today (23 February 2021) in Nature Communications, details the first evidence of gene regulation in the transit of eggs from the ovaries to the uterus in mammals. The findings highlight Adgrd1 as a promising target for future studies in humans, in order to search for genetic mutations or anomalies that may help to explain why ectopic pregnancy occurs.

Each month, a single egg is released from one of a woman’s ovaries and travels to the uterus via the fallopian tubes (also known as oviducts). The egg ‘pauses’ at a certain location, called the ampullary-isthmic junction, for several days. If sperm are present, this is where fertilization occurs. The egg then continues its journey and, if it has been fertilized, will implant into the wall of the uterus. This process is common to many mammal species, including mice.

Ectopic pregnancies occur when a fertilized egg implants and develops outside of the uterus, usually in one of the fallopian tubes. This is known as a tubal pregnancy and it is not possible to save the pregnancy once this occurs*. Ectopic pregnancy affects one to two per cent of all conceptions in the United States and Europe, and is the most common cause of pregnancy-related death in the first trimester.

Movement of the egg is controlled by several factors, including tiny hairs called cilia on the surface of the fallopian tubes which wave the egg towards the uterus, muscle contractions, and the flow of oviductal fluid. But the biology of the egg’s journey is not fully understood, particularly how the ‘pause’ at the ampullary-isthmic junction is regulated.

In this study, researchers at the Wellcome Sanger Institute set out to identify genes required for female fertility whose function was not fully understood. They analysed the International Mouse Phenotyping Consortium database, which contains data on mice that have had certain genes suppressed or ‘switched off’, and identified Adgrd1 as a gene of interest.

When they examined female mice that lacked a functional Adgrd1 gene, they observed that although the mice ovulated normally and fertilisation took place, the eggs could not move past the ampullary-isthmic junction and implanted outside of the uterus**.

To find out why, they investigated the movement of cilia in the fallopian tubes, muscle contractions and the flow of oviductal fluid. Scientists at Genentech, a member of the Roche Group, conducted a genetic screen to determine the molecular mechanisms at play.

The team concluded that the suppression of Adgrd1 activity affected the flow of oviductal fluid, preventing the egg from continuing its journey to the uterus after the ‘pause’ at the ampullary-isthmic junction.

“The flow of oviductal fluid in mammals is somewhat counterintuitive, in that it flows in the opposite direction to the egg’s direction of travel. What we’ve discovered in this study is that the strength of this flow is normally downregulated by the Adgrd1 gene. But when Adgrd1 is suppressed, the flow is not reduced and the egg cannot seem to move past the ampullary-isthmic junction.”

— Dr Enrica Bianchi, first author of the study from the Wellcome Sanger Institute

“The molecular cues that dictate G protein-coupled receptor signalling and biological functions still remain poorly understood, despite these proteins represent main drug targets. The identification of Plxdc2 as an activating ligand for Adgrd1 sheds light on the biology of this previously orphan receptor and opens new avenues for the treatment of ectopic pregnancy.”

Nadia Martinez-Martin, a senior author of the paper from biotechnology company Genentech, a member of the Roche Group

Though this study was conducted in mice, a species in which ectopic pregnancy does not occur, the reproductive biology of humans, mice and other mammals share many of the same mechanisms. The next step is to conduct further studies in humans, to see if the role of Adgrd1 is the same and whether mutation or loss of function of this gene correlates with incidence of ectopic pregnancy.

“Though several risk factors of ectopic pregnancy are known, the precise genetic and molecular mechanisms behind the condition have remained unclear. The discovery of the function of Adrgd1 in oviductal fluid regulation, and the consequences of its absence, provides an important clue for researchers studying the causes of ectopic pregnancy in future.”

Dr Gavin Wright, senior author of the study from the Wellcome Sanger Institute

Featured image credit: adobestock


Reference: Bianchi, E., Sun, Y., Almansa-Ordonez, A. et al. Control of oviductal fluid flow by the G-protein coupled receptor Adgrd1 is essential for murine embryo transit. Nat Commun 12, 1251 (2021). https://www.nature.com/articles/s41467-021-21512-w https://doi.org/10.1038/s41467-021-21512-w


Provided by Wellcome Sanger Institute

Researchers Uncover Link Between Racial, Ethnic & Socioeconomic Factors & Likelihood of Getting Effective Treatment for Atrial Fibrillation

Findings show Black, Latinx, and lower income patients receive less rhythm control

Even though the use of rhythm control strategies for treating Paroxysmal Atrial Fibrillation (AF), a common abnormal heart rhythm, have increased overall in the United States, patients from racial and ethnic minority groups and those with lower income were less likely to receive rhythm control treatment – often the preferred treatment – according to new research from the Perelman School of Medicine at the University of Pennsylvania. The study is published in the JAMA Network Open.

“Research has demonstrated the pervasive impact of structural racism on health outcomes among minoritized patients. We know, for instance, that there is less use of novel cardiovascular therapies among Black, Latinx, and patients of lower socioeconomic status,” said the study’s lead author, Lauren Eberly, MD, MPH, a cardiology fellow at the University of Pennsylvania. “That’s why we wanted to evaluate the rates of antiarrhythmic drugs and catheter ablation and investigate for the presence of inequities to see how we can do better from an equity standpoint.”

Atrial Fibrillation is the most common sustained heart rhythm disorder, and is the cause of significant complications including heart failure and stroke, which can be deadly for some patients. The two forms of rhythm control are antiarrhythmic drugs and catheter ablation, which aims to eliminate the sources of atrial fibrillation. Evidence suggests that when doctors pursue these rhythm control strategies early in the course of the patient’s disease, they are more likely to successfully control the condition, and long term cardiovascular outcomes are improved.

Researchers examined data from October 2015 to June 2019 from more than 100,000 diverse, commercially insured patients, and found that from 2016 to 2019 the cumulative percentage of patients treated with antiarrhythmic drugs and catheter ablation increased from 1.6 percent to 3.8 percent. Despite this overall increase, patients with Latinx ethnicity and those who lived in zip codes with lower median household income were less likely to receive catheter ablation treatment, and Black and lower-income patients were less likely to be prescribed antiarrhythmic drugs or treated with catheter ablation.

Overall, patients living in areas with median household incomes of less than $50,000 were 39 percent less likely to receive catheter ablation compared with those with a median household income of $100,000 or more.

According to researchers, the number of cardiology visits by each patient was one of the strongest factors associated with rhythm control and catheter ablation use, stressing the importance of access to care. The findings suggest that reduced access to specialty care, including cardiovascular care for Black patients, is a potential reason for differences in treatments.

“As evidence builds regarding the benefits of early rhythm control and particularly catheter ablation, we must ensure that all our patients benefit equally” said the study’s senior author, David Frankel, MD, Associate Professor of Medicine and Director of the Cardiac Electrophysiology Fellowship.

Eberly also hopes that in addition this awareness will push primary care providers and non-cardiac providers to more readily consider rhythm-control strategies or referral to a specialist, particularly for those patients who have been historically marginalized by the healthcare system.

Funding was provided by the Mark Marchlinski Research and Education Fund.


Reference: Lauren A. Eberly, Lohit Garg, Lin Yang, et al, “Racial/Ethnic and Socioeconomic Disparities in Management of Incident Paroxysmal Atrial Fibrillation”, JAMA Netw Open. 2021;4(2):e210247. doi: 10.1001/jamanetworkopen.2021.0247


Provided by Penn Medicine

Plant-Based Protein Lowers Risk of Premature Death, Heart Disease, Dementia-Related Death (Food)

Postmenopausal women who consumed more plant-based protein have a lower risk of premature death, cardiovascular disease, and dementia-related death, according to a study published online in the Journal of the American Heart Association.

Researchers compared types of protein intake with mortality for more than 100,000 post-menopausal women from the Women’s Health Initiative. Those who consumed the most plant-based protein from nuts, legumes, and other plant-based foods were less likely to die from cardiovascular disease, dementia, and all causes when compared to those who consumed the least amount of plant-based protein. Consuming eggs, dairy products, and red meat was associated with a higher risk of death from heart disease, cancer, and dementia.

Results also showed swapping animal protein with plant-based protein sources lowered mortality risk. Saturated fat, cholesterol, and heterocyclic amines found in animal products may contribute to disease development associated with mortality. The authors suggest that dietary guidelines recommend healthier types of protein sources for long-term health.

Featured image credit: Gettyimages


References

Sun Y, Liu B, Snetselaar LG, et al. Association of major dietary protein sources with all-cause and cause-specific mortality: Prospective cohort study. J Am Heart Assoc. 2021 Feb 24;e015553. doi: 10.1161/JAHA.119.015553


Provided by Physicians Committee for Responsible Medicine

New ‘Home-Grown’ Coronavirus Variant Found in New York City Region (Medicine)

A new SARS-CoV-2 lineage that shares worrisome similarities with other recent variants of concern is on the rise in New York City, according to a study by scientists at Columbia University Vagelos College of Physicians and Surgeons. 

The study(link is external and opens in a new window), which has not been peer reviewed, has been posted on the preprint server medRxiv. 

So far, more than 80 cases of the home-grown variant have been identified in patients across the tri-state area, including Connecticut and Westchester County.

The prevalence of the new variant—called B.1.526—has been steadily increasing since it first appeared in samples collected in Nov. 2020. In Jan. 2021, B.1.526 represented about 3% of samples analyzed by the researchers, rising to 12.3% by mid-February. The cases they found are scattered throughout the New York City area.

Initially, we thought we’d find alot of other known Lineages. Instead we found high numbers of this home-grown lineage.

The researchers also searched publicly available databases and found COVID-19 cases caused by B.1.526 and closely related strains are emerging predominantly in the northeastern United States, as suggested by other researchers in a study recently posted to bioRxiv.

“It’s not just one cluster, which means the lineage is probably spreading widely through the region,” says Anne-Catrin Uhlemann, MD, PhD, associate professor of medicine in the Division of Infectious Diseases, who led the study with David Ho, MD, director of the Aaron Diamond AIDS Research Center and the Clyde ‘56 and Helen Wu Professor of Medicine.

The researchers started to look for key mutations found in variants of concern in the New York City region in January and have analyzed over 1,100 samples. “Initially, we thought we’d find a lot of the other known lineages,” Uhlemann says. Though a couple variants, originally identified in South Africa and Brazil, were detected, “we didn’t find the high numbers we expected. Instead we found high numbers of this home-grown lineage,” she says.

Similarities with other variants of concern

The impact of the new B.1.526 variant on transmissibility, disease severity, and risk of reinfection is not yet known. 

But the Columbia study shows that B.1.526 shares some worrying characteristics with B.1.351, a variant first identified in South Africa, and P.1., first identified in Brazil, that are less susceptible to some treatments and vaccines. 

Of prime concern is a change in one area of the virus’s spike protein, called E484K, that is present in all three variants. The E484K mutation is believed to weaken the body’s immune response to the virus.

A recent study(link is external and opens in a new window) by Ho found antibodies from vaccinated people are less effective at neutralizing the B.1.351 virus—and that the effect is primarily caused by the E484K mutation.

The E484K mutation is also responsible, he found, for the drop in effectiveness of certain monoclonal antibody treatments against the B.1.351 variant.

Variants with the E484K mutation may also cause reinfection in people who were infected previously with earlier variants of the virus. In the current report, one of the individuals infected with the new B.1.526 variant had a previously documented SARS-CoV-2 infection without the E484K mutation, and the researchers are currently working to determine the potential origins of this local lineage.

What’s next?

In the coming weeks, the scientists plan to ramp up sequencing efforts to around 100 samples per day to continue surveillance of the new variants, including B.1.526. 

“We are also finding many cases of the B.1.1.7 variant, originally identified in the U.K, and it’s possible those cases will double—but it’s hard to know which variant will cause the biggest problem,” Uhlemann says. “Increasing our genomic sequencing effort will help us better understand the impact of the new variant and keep our eyes open for new variants that may pop up in our area.”

The researchers also are working to culture the live variant to learn more about its vulnerability to vaccines and monoclonal antibody treatments, and its potential for reinfection.

Physical distancing and masks will slow the spread of all variants and we need to double down on those efforts

“The rise of these variants shows that we may be chasing after SARS-CoV-2 for some time,” Ho says. “Unfortunately, this pandemic may not go away so easily with the advent of the vaccines.”

“It’s worrying that in the New York City region, case numbers don’t seem to be declining as rapidly as in other areas of the country,” Uhlemann says, “Physical distancing and masks will slow the spread of all variants, and we need to double down on those efforts.”


Reference: Medini K. Annavajhala, Hiroshi Mohri, Jason E. Zucker, Zizhang Sheng, Pengfei Wang, Angela Gomez-Simmonds, David D. Ho, Anne-Catrin Uhlemann, “A Novel SARS-CoV-2 Variant of Concern, B.1.526, Identified in New York”, medRxiv 2021.02.23.21252259; doi: https://doi.org/10.1101/2021.02.23.21252259


Provided by Columbia University Irving Medical Center

What Are The Effects Of Different Dark Energies On the Mass Of Wormholes? (Cosmology / Astronomy)

In recent observations it is strongly believed that the universe is experiencing an accelerated expansion. The type Ia Supernovae and Cosmic Microwave Background (CMB) observations have shown the evidences to support cosmic acceleration. This acceleration is caused by some unknown matter which has the property that positive energy density and negative pressure satisfying ρ + 3p < 0 is dubbed as “dark energy” (DE). If ρ + p < 0, it is dubbed as “phantom energy”. The combined astrophysical observations suggests that universe is spatially flat and the dark energy occupies about 70% of the total energy of the universe, the contribution of dark matter is ∼ 26%, the baryon is 4% and negligible radiation. A cosmological property in which there is an infinite expansion in scale factor in a finite time termed as ‘Big Rip’. In the phantom cosmology, big rip is a kind of future singularity in which the energy density of phantom energy will become infinite in a finite time. To realize the Big Rip scenario the condition ρ + p < 0 alone is not sufficient. Distinct data on supernovas showed that the presence of phantom energy with – 1.2 < w < – 1 in the Universe is highly likely. In this case the cosmological phantom energy density grows at large times and disrupts finally all bounded objects up to subnuclear scale.

A wormhole is a feature of space that is essentially a “shortcut” from one point in the universe to another point in the universe, allowing travel between them that is faster than it would take light to make the journey through normal space. So the wormholes are tunnels in spacetime geometry that connect two or more regions of the same spacetime or two different spacetimes. Wormholes may be classified into two categories – Euclidean wormholes and Lorentzian wormholes. The Euclidean wormholes arise in Euclidean quantum gravity and the Lorentzian wormholes which are static spherically symmetric solutions of Einstein’s general relativistic field equations. In order to support such exotic wormhole geometries, the matter violating the energy conditions (null, weak and strong), but average null energy condition is satisfied in wormhole geometries. For small intervals of time, the weak energy condition (WEC) can be satisfied.

Ujjal Debnath and colleagues in their work studied effects of accretion of the dark energies onto Morris-Thorne wormhole using a dark-energy accretion model for wormholes which have been obtained by generalizing the Michel theory. They found that for quintessence like dark energy, the mass of the wormhole decreases and phantom like dark energy, the mass of wormhole increases.

They have also assumed recently proposed two types of dark energy like variable modified Chaplygin gas (VMCG) and generalized cosmic Chaplygin gas (GCCG). They obtained the expression of wormhole mass in both cases and found that the mass of the wormhole is finite at late universe. Their dark energy fluids violate the strong energy condition (ρ + 3p < 0 in late epoch), but do not violate the weak energy condition (ρ + p > 0). So the models drive only quintessence scenario in late epoch, but do not generate the phantom epoch (in their choice). So wormhole mass decreases during evolution of the universe for these two dark energy models.

Since their considered dark energy candidates do not violate weak energy condition, so the dynamical mass of the wormhole are decaying by the accretion of their considered dark energies, though the pressures of the dark energies are outside the wormhole. From figures 1 and 2, they observed that the wormhole mass decreases as z increases for both VMCG and GCCG, which accrete onto the wormhole in our expanding universe.

Figs. 1 and 2 show the variations of wormhole mass M against redshift z for VMCG and GCCG models.

Next they have assumed 5 kinds of parametrizations (Models I-V) of well known dark energy models (some of them are Linear, CPL, JBP models). These models generate both quintessence and phantom scenarios for some restrictions of the parameters. So if these dark energies accrete onto the wormhole, then for quintessence stage, wormhole mass decreases upto a certain value (finite value) and then again increases to infinite value for phantom stage during whole evolution of the universe. They also showed these results graphically clearly. Figures 3-7 shows the mass of wormhole first decreases to finite value and then increases to infinite value.

Figs. 3-7 show the variations of wormhole mass M against redshift z for Models I-V respectively

In future work, it will be interesting to show the natures of mass for various types of wormhole models if different kinds of dark energies accrete upon wormhole in accelerating universe also.

— said debnath, lead author of the study.

Reference: Debnath, U. Accretions of various types of dark energies onto Morris–Thorne wormhole. Eur. Phys. J. C 74, 2869 (2014). https://link.springer.com/article/10.1140/epjc/s10052-014-2869-4 https://doi.org/10.1140/epjc/s10052-014-2869-4


Copyright of this article totally belongs to our author S. Aman. One is allowed to reuse it only by giving proper credit either to him or to us

Measuring the tRNA World (Biology)

Researchers have developed a method to quantify transfer RNAs

Transfer RNAs (tRNAs) deliver specific amino acids to ribosomes during translation of messenger RNA into proteins. The abundance of tRNAs can therefore have a profound impact on cell physiology, but measuring the amount of each tRNA in cells has been limited by technical challenges. Researchers at the Max Planck Institute of Biochemistry have now overcome these limitations with mim-tRNAseq, a method that can be used to quantify tRNAs in any organism and will help improve our understanding of tRNA regulation in health and disease.

A cell contains several hundred thousand tRNA molecules, each of which consists of only 70 to 90 nucleotides folded into a cloverleaf-like pattern. At one end, tRNAs carry one of the twenty amino acids that serve as protein building blocks, while the opposite end pairs with the codon specifying this amino acid in messenger RNA during translation. Although there are only 61 codons for the twenty amino acids, cells from different organisms can contain hundreds of unique tRNA molecules, some of which differ from each other by only a single nucleotide. Many nucleotides in tRNAs are also decorated with chemical modifications, which help tRNAs fold or bind the correct codon.

The levels of individual tRNAs are dynamically regulated in different tissues and during development, and tRNA defects are linked to neurogical diseases and cancer. The molecular origins of these links remain unclear, because quantifying the abundance and modifications of tRNAs in cells has long remained a challenge. The team of Danny Nedialkova at the MPI of Biochemistry has now developed mim-tRNAseq, a method that accurately measures the abundance and modification status of different tRNAs in cells.

Modification roadblocks and resolutions

To measure the levels of multiple RNAs simultaneously, scientists use an enzyme called reverse transcriptase to first rewrite RNA into DNA. Millions of these DNA copies can then be quantified in parallel by high-throughput sequencing. Rewriting tRNAs into DNA has been tremendously hard since many tRNA modifications block the reverse transcriptase, causing it to stop synthesizing DNA.

“Many researches have proposed elegant solutions to this problem, but all of them relieve only a fraction of the modification roadblocks in tRNAs”, explains Danny Nedialkova, Max Planck Research Group Leader at the Max Planck Institute of Biochemistry. “We noticed that one specific reverse transcriptase seemed to be much better at reading through modified tRNA sites. By optimizing the reaction conditions, we could significantly improve the enzyme’s efficiency, enabling it to read through nearly all tRNA modification roadblocks”, adds Nedialkova. This made it possible to construct DNA libraries from full-length tRNA copies and use them for high-throughput sequencing.

The mim-tRNAseq computational toolkit

The analysis of the resulting sequencing data also presented significant challenges. “We identified two major issues: the first one is the extensive sequence similarity between different tRNA transcripts”, explains Andrew Behrens, PhD student in Nedialkova’s group and first author of the paper. “The second one comes from the fact that an incorrect nucleotide (a misincorporation) is introduced at many modified sites during reverse transcription. Both make it extremely challenging to assign each DNA read to the tRNA molecule it originated from”, adds Behrens.

The team tackled these issues with novel computational approaches, including the use of modification annotation to guide accurate read alignment. The resulting comprehensive toolkit is packaged into a freely available pipeline for alignment, analysis and visualization of tRNA-derived sequencing data (https://github.com/nedialkova-lab/mim-tRNAseq). Researchers can use mim-tRNAseq to not only measure tRNA abundance, but also to map and quantify tRNA modifications that induce nucleotide misincorporations by the reverse transcriptase. “mim-tRNAseq opens up myriad possibilities moving forward,” says Nedialkova. “We expect it will help us and others to tackle many outstanding questions about tRNA biology in health and disease.”

Featured image: Artistic representation of tRNAs © Heather Jenkins


Reference: A. Behrens, G. Rodschinka, D.D. Nedialkova, “High-resolution quantitative profiling of tRNA abundance and modification status in eukaryotes by mim-tRNAseq”, Molecular Cell, February 2021. Link to paper


Provided by Max Planck Gesellschaft

Quantum Quirk Yields Giant Magnetic Effect, Where None Should Exist (Quantum)

Study opens window into the landscape of extreme topological matter

In a twist befitting the strange nature of quantum mechanics, physicists have discovered the Hall effect — a characteristic change in the way electricity is conducted in the presence of a magnetic field — in a nonmagnetic quantum material to which no magnetic field was applied.

The discovery by researchers from Rice University, Austria’s Vienna University of Technology (TU Wien), Switzerland’s Paul Scherrer Institute and Canada’s McMaster University is detailed in a paper in the Proceedings of the National Academy of Sciences. Of interest are both the origins of the effect, which is typically associated with magnetism, and its gigantic magnitude — more than 1,000 times larger than one might observe in simple semiconductors.

Rice study co-author Qimiao Si, a theoretical physicist who has investigated quantum materials for nearly three decades, said, “It’s really topology at work,” referring to the patterns of quantum entanglement that give rise the unorthodox state.

The material, an exotic semimetal of cerium, bismuth and palladium, was created and measured at TU Wien by Silke Bühler-Paschen, a longtime collaborator of Si’s. In late 2017, Si, Bühler-Paschen and colleagues discovered a new type of quantum material they dubbed a “Weyl-Kondo semimetal.” The research laid the groundwork for empirical investigations, but Si said the experiments were challenging, in part because it wasn’t clear “which physical quantity would pick up the effect.”

In April 2018, Bühler-Paschen and TU Wien graduate student Sami Dzsaber, the study’s first author, dropped by Si’s office while attending a workshop at the Rice Center for Quantum Materials (RCQM). When Si saw Dzsaber’s data, he was dubious.

“Upon seeing this, everybody’s first reaction is that it is not possible,” he said.

To appreciate why, it helps to understand both the nature and the 1879 discovery of Edwin Hall, a doctoral student who found that applying a magnetic field at a 90-degree angle to conducting wire produced a voltage difference across the wire, in the direction perpendicular to both the current and the magnetic field. Physicists eventually discovered the source of the Hall effect: The magnetic field deflects the motion of passing electrons, pulling them toward one side of the wire. The Hall effect is a standard tool in physics labs, and devices that make use of it are found in products as diverse as rocket engines and paintball guns. Studies related to the quantum nature of the Hall effect captured Nobel Prizes in 1985 and 1998.

Photograph of a single crystal of a nonmagnetic topological material of cerium, bismuth and palladium known as a Weyl-Kondo semimetal that physicists at Vienna University of Technology used to measure the Hall effect — a characteristic change in the way electricity is conducted in the presence of a magnetic field — with no magnetic field applied. (Photo by S. Dzsaber/TU Wien)

Dzsaber’s experimental data clearly showed a characteristic Hall signal, even though no magnetic field was applied.

“If you don’t apply a magnetic field, the electron is not supposed to bend,” Si said. “So, how could you ever get a voltage drop along the perpendicular direction? That’s why everyone didn’t believe this at first.”

Experiments at the Paul Scherrer Institute ruled out the presence of a tiny magnetic field that could only be detected on a microscopic scale. So the question remained: What caused the effect?

“In the end, all of us had to accept that this was connected to topology,” Si said.

In topological materials, patterns of quantum entanglement produce “protected” states, universal features that cannot be erased. The immutable nature of topological states is of increasing interest for quantum computingWeyl semimetals, which manifest a quasiparticle known as the Weyl fermion, are topological materials.

So are the Weyl-Kondo semimetals Si, Bühler-Paschen and colleagues discovered in 2018. Those feature both Weyl fermions and the Kondo effect, an interaction between the magnetic moments of electrons attached to atoms inside the metal and the spins of passing conduction electrons.

“The Kondo effect is the quintessential form of strong correlations in quantum materials,” Si said in reference to the correlated, collective behavior of billions upon billions of quantum entangled particles. “It qualifies the Weyl-Kondo semimetal as one of the rare examples of a topological state that’s driven by strong correlations.

“Topology is a defining characteristic of the Weyl-Kondo semimetal, and the discovery of this spontaneous giant Hall effect is really the first detection of topology that’s associated with this kind of Weyl fermion,” Si said.

Physicists Sami Dzsaber and Silke Bühler-Paschen of Vienna University of Technology (Photo by F. Aigner/TU Wien)

Experiments showed that the effect arose at the characteristic temperature associated with the Kondo effect, indicating the two are likely connected, Si said.

“This kind of spontaneous Hall effect was also observed in contemporaneous experiments in some layered semiconductors, but our effect is more than 1,000 times larger,” he said. “We were able to show that the observed giant effect is, in fact, natural when the topological state develops out of strong correlations.”

Si said the new observation is likely “a tip of the iceberg” of extreme responses that result from the interplay between strong correlations and topology.

He said the size of the topologically generated Hall effect is also likely to spur investigations into potential uses of the technology for quantum computation.

“This large magnitude, and its robust, bulk nature presents intriguing possibilities for exploitation in topological quantum devices,” Si said.

Si is the Harry C. and Olga K. Wiess Professor in Rice’s Department of Physics and Astronomy and director of RCQM. Bühler-Paschen is a professor at TU Wien’s Institute for Solid State Physics.

Study co-authors include Sarah Grefe and Hsin-Hua Lai, both of Rice; Xinlin Yan, Mathieu Taupin, Gaku Eguchi, Andrey Prokofiev and Peter Blaha of TU Wien; Toni Shiroka of the Paul Scherrer Institute; and Oleg Rubel of McMaster University.

The research was funded by the Austrian Science Fund, the European Union’s Horizon 2020 Research and Innovation Program, the Swiss National Science Foundation, the National Science Foundation, the Welch Foundation and an Ulam Scholarship from the Center for Nonlinear Studies at Los Alamos National Laboratory.

RCQM leverages global partnerships and the strengths of more than 20 Rice research groups to address questions related to quantum materials. RCQM is supported by Rice’s offices of the provost and the vice provost for research, the Wiess School of Natural Sciences, the Brown School of Engineering, the Smalley-Curl Institute and the departments of Physics and Astronomy, Electrical and Computer Engineering, and Materials Science and NanoEngineering.

Featured image: Rice University theoretical physicists (from left) Hsin-Hua Lai, Qimiao Si and Sarah Grefe worked with experimental collaborators at Vienna University of Technology to understand topological features of a nonmagnetic Weyl-Kondo semimetal allowed it to produce a giant Hall effect in the absence of a magnetic field. (Photo by Jeff Fitlow/Rice University)


Reference: Sami Dzsaber, Xinlin Yan, Mathieu Taupin, Gaku Eguchi, Andrey Prokofiev, Toni Shiroka, Peter Blaha, Oleg Rubel, Sarah E. Grefe, Hsin-Hua Lai, Qimiao Si, Silke Paschen, “Giant spontaneous Hall effect in a nonmagnetic Weyl–Kondo semimetal”, Proceedings of the National Academy of Sciences Feb 2021, 118 (8) e2013386118; DOI: 10.1073/pnas.2013386118


Provided by Rice University

Cancer: A New Killer Lymphocyte Enters the Ring (Medicine)

A team from SCCL has discovered that CD4 T lymphocytes, which usually play a supporting role in fighting cancer cells, also have the power to destroy them.

Treatments for beating tumours are mainly based on CD8 T lymphocytes, which specialise in detecting and eliminating intracellular infections and in killing cancer cells. A large proportion of patients, however, do not respond to these treatments. This prompted a research team from the Swiss Cancer Centre Léman (SCCL, Switzerland) to bring together the universities of Geneva (UNIGE) and Lausanne (UNIL), the Ludwig Institute for Cancer Research (LICR), EPFL and CHUV to investigate CD4 T lymphocytes. While these play a supporting role with CD8 T cells, their ability to eliminate tumour cells directly has been a matter of controversy. Using innovative nanoimaging technologies designed at the EPFL laboratory, the scientists found that when the CD4 T lymphocytes were directly put in close contact to the cancer cells, up to a third of them could also kill them. This discovery, the subject of an article in Science Advances, is significant and broadens the therapeutic perspectives based on administering CD4 T lymphocytes to patients who are resistant to conventional therapies.

When cancer cells proliferate in our bodies, our immune system kicks in. The first line of fighters capable of destroying tumour cells are CD8 T lymphocytes known as cytotoxic T cells, backed up by CD4 T lymphocytes. The latter secrete factors that help the former in many ways. “That’s why lots of cancer treatments are based on CD8 T lymphocytes,” begins Camilla Jandus, last author of the study and a professor in the Department of Pathology and Immunology in UNIGE’s Faculty of Medicine and adjunct scientist at LICR. “Unfortunately, some patients don’t respond to these treatments, and so we have to find new ones.”

The SCCL team turned their focus to CD4 T lymphocytes, which offer invaluable support to our immune system, as Pedro Romero, a professor in the Department of Fundamental Oncology in UNIL’s Faculty of Medicine and Biology, explains: “These have a much wider spectrum of functional specialisations than CD8 T lymphocytes, and for a long time we didn’t know for sure whether they had the capacity to differentiate into killer lymphocytes.”

20,000 individual “boxing rings”

To address this question, the scientists examined CD4 T lymphocytes from around twenty patients with melanoma who were being treated at CHUV. “Although melanoma isn’t the most common skin cancer, it is the deadliest, and it’s particularly sensitive to immunotherapies,” spells out Professor Jandus. The researchers isolated the CD4 T lymphocytes from both the blood and fragments of the tumours with the idea of comparing them directly. Dissociated tumour cells and CD4 T cells were co-incubated to observe their behaviour individually. Observation tools were then required to provide highly-advanced resolution down to the single cell level. “We created chips of over 20,000 mini-wells of 65 picolitres (1 picolitre = 10-12 litre) that can accommodate a CD4 T cell and a tumour cell in each of them, and function like boxing rings,” says Hatice Altug, a professor in EPFL’s Bionanophotonic Systems Laboratory. The researchers then photographed all these thousands wells simultaneously every five minutes for 24 hours in order to observe the interactions occurring between the two cells from a large set of pairs. “We know that it takes about two and a half hours for a CD8 to kill a tumour cell, and we decided to observe these boxing rings for 24 hours without knowing how, and if, the CD4s would react,” continues Professor Altug.

A third of the CD4s emerged victorious

To the great satisfaction of the scientists, the high-throughput integration of dynamic imaging data showed that up to a third of the CD4 T lymphocytes succeeded in killing the tumour cell to which they were closely linked within five hours. As Professor Romero stresses: “These direct observations at the level of individual lymphocytes, which were revealed for the first time at such a level of sensitivity, definitively confirm the existence of CD4 T lymphocytes capable of killing tumour cells. And this happens while the tumour cells sometimes manage to divert them from their function of providing protective support to make allies of them.”

By analysing the killer variety of CD4 T lymphocytes in detail, the scientists found that they expressed the SLAMF7 molecule, which promoted their tumor killer activity. “That’s why we’re now going to isolate and cultivate in vitro the best killer variety of CD4 T lymphocytes so we can turn them into a veritable army of trillions of cells, which we can then inject into patients on whom CD8-based treatments don’t work,” says Dr Jandus. The human body naturally has only a small number of CD4 T lymphocytes directed against tumours, and not enough to defeat them. “The ability to visualise this close combat with our picowell chip paves the way for expanding the arsenal in the fight against cancer, which we now need to develop,” concludes Professor Altug.

Featured image: The fight between CD4 T-lymphocytes (in blue) against tumour cells (in orange). © 2021 EPFL Hatice Altug


Reference: Amélie Cachot, Mariia Bilous, Yen-Cheng Liu, Xiaokang Li, Margaux Saillard, Mara Cenerenti, Georg Alexander Rockinger, Tania Wyss, Philippe Guillaume, Julien Schmidt, Raphaël Genolet, Giuseppe Ercolano, Maria Pia Protti, Walter Reith, Kalliopi Ioannidou, Laurence de Leval, Joseph A. Trapani, George Coukos, Alexandre Harari, Daniel E. Speiser, Alexander Mathis, David Gfeller, Hatice Altug, Pedro Romero, Camilla Jandus, “Tumor-specific cytolytic CD4 T cells mediate immunity against human cancer”, Science Advances 26 Feb 2021: Vol. 7, no. 9, eabe3348 DOI: 10.1126/sciadv.abe3348


Provided by University of Geneva