“Each of these diseases has a unique protein tangle, or fibril, associated with it,” said Anthony Fitzpatrick, PhD, principal investigator at Columbia’s Zuckerman Institute. “These proteins associated with diseases have their own shapes and behaviors,” added Dr. Fitzpatrick, also an assistant professor of biochemistry and molecular biophysics at Columbia University Irving Medical Center and a member of Columbia’s Taub Institute for Research on Alzheimer’s Disease and the Aging Brain.

Published today in Cell, the research by Dr. Fitzpatrick and an international team of 22 collaborators reveals a new fibril in diseased brains, one formed by a protein normally busy cleaning cells.

“We have a surprising and provocative result that we hope could have some bearing on managing neurodegenerative diseases,” said undergraduate Andrew Chang, a co-first author on the paper in the Fitzpatrick lab. Drug researchers have long pursued the tangle-forming proteins as targets for new medicines, but this pursuit so far has largely delivered disappointing results.

Fibril-associated diseases, some common and some rare, collectively affect millions of people around the world. Their incidence is slated to increase as the population grows and people live longer. Untangling what is going on in these neurodegenerative diseases has a personal facet for Dr. Fitzpatrick: He lost an uncle to one of them, progressive supranuclear palsy (PSP).

“We have found that a protein called TMEM106B can form fibrils, and this behavior was not known before,” said Xinyu Xiang, formerly a member of the Fitzpatrick lab at the Zuckerman Institute and now a graduate student at Stanford University’s Department of Structural Biology. “This protein is a core component of lysosomes and endosomes, which are organelles that clean up the junk that builds up in our cells as we get older.”

Normally, TMEM106B molecules span the membranes of those waste-management organelles. In a feat of laboratory sleuthing, Fitzpatrick’s team discovered that TMEM106B molecules can split into two fragments. Fragments inside the organelles can then self-assemble into what the researchers suspect could be cell-hobbling fibrils.

To make this discovery, the researchers first extracted proteins from brain tissue donated by 11 patients who had died from three neurodegenerative diseases associated with misfolded proteins: PSP, dementia with Lewy bodies (DLB) and frontotemporal lobar degeneration (FTLD). FTLD is the most prevalent form of dementia for those under 60 years of age.

“It’s so motivating to remember that the only way we can do this research is because of people who generously donated their brains,” said Marija Simjanoska, a co-first author and one of the three undergraduates working on the project.

Co-corresponding author Ian Mackenzie, MD, of the University of British Columbia, and co-authors Dennis Dickson, MD, and Leonard Pertrocelli, PhD, of the Mayo Clinic in Florida, helped procure this precious research resource. Joining Drs. Fitzpatrick and Mackenzie as co-corresponding authors on the paper is Michael Stowell, PhD, of the University of Colorado, Boulder. Filling out the 23-member team are researchers from several other institutions, including three in Belgium.

With a world-class cryogenic electron microscope (cryo-EM), the team took snapshots of individual protein molecules at many different angles. From these, the researchers constructed three-dimensional models of the protein in atomic detail. Those models, in turn, helped the researchers identify TMEM106B by making educated guesses about the exact sequence of the protein’s amino-acid building blocks. Much in the way letters string into words with specific meanings, different amino-acid molecules build into proteins, each with its own shape and function.

The researchers fully expected that one of the long-known fibril-forming proteins, such as the tau protein in Alzheimer’s disease, would end up matching with the models from the cryo-EM data. Instead, the matching exercise, which involved searching in a massive database of protein sequences, delivered a head-turning result.

The researchers found that the mysterious protein matched a 135-amino-acid fragment of TMEM106B. That was an exciting revelation because this same protein was identified more than a decade ago in a broad hunt for genes potentially associated with FTLD.

So far, the data in hand shows only that TMEM106B fibrils are present in diseased brain tissue, not that the fibrils cause the diseases. Still, Dr. Fitzpatrick points out, the prevalence of TMEM106B fibrils in tissue from different brain diseases, combined with the protein’s normal place in lysosomes and endosomes, points toward a possible disease-causing role.

In their Cell paper, the researchers speculate that the formation of TMEM106B fibrils disrupts lysosome function, which, in turn, promotes the formation of fibrils made of the other known fibril-forming proteins. These malfunctions could kill brain cells, leading to dementia, movement problems, speech pathologies and other symptoms of Alzheimer’s, PSP, FTLD and other brain diseases with telltale protein tangles.

“We now have a promising new lead,” said Dr. Fitzpatrick. “It could point towards a common thread linking a range of neurodegenerative diseases and could open the way to new interventions.”

This work was supported by the National Institutes of Health (NIH)/National Institute of Neurological Disorder and Stroke (UO1NS110438, U54NS110435); the Association for Frontotemporal Degeneration; Canadian Institutes of Health Research (74580); and MCDB Neurodegenerative Disease Fund.

Black holes are some of the most mystifying objects in our universe, largely due to the fact that their inner-workings are hidden behind a completely obscuring veil — the black hole’s event horizon.

In 1974, Stephen Hawking added more mystique to the character of black holes by showing that, once quantum effects are considered, a black hole isn’t really black at all but, instead, emits radiation, as if it was a hot body, gradually losing mass in the so-called “Hawking evaporation process.” Further, Hawking’s calculations showed that the emitted radiation is quantum mechanically entangled with the bowels of the black hole itself. This entanglement is the quantum signature of the Hawking effect. This astounding result is difficult, if not impossible, to be tested on astrophysical black holes, since the faint Hawking radiation gets overshined by other sources of radiation in the cosmos.

On the other hand, in the 1980’s, a seminal article by William Unruh established that the spontaneous production of entangled Hawking particles occurs in any system that can support an effective event horizon. Such systems generally fall under the umbrella of “analog gravity systems” and opened a window for testing Hawking’s ideas in the laboratory.

Serious experimental investigations into analog gravity systems — made of Bose-Einstein condensates, non-linear optical fibers, or even flowing water — have been underway for more than a decade. Stimulated and spontaneously-generated Hawking radiation has recently been observed in several platforms, but measuring entanglement has proved elusive due to its faint and fragile character.

“We show that, by illuminating the horizon, or horizons, with appropriately chosen quantum states, one can amplify the production of entanglement in Hawking’s process in a tunable manner,” said Associate Professor Ivan Agullo. “As an example, we apply these ideas to the concrete case of a pair of analog white-black holes sharing an interior and produced within a non-linear optical material.”

“Many of the quantum information tools used in this research were from my graduate research with Professor Jonathan P. Dowling,” said 2021 PhD alumnus Anthony Brady, postdoctoral researcher at the University of Arizona. “Jon was a charismatic character, and he brought his charisma and unconventionality into his science, as well as his advising. He encouraged me to work on eccentric ideas, like analog black holes, and see if I could meld techniques from various fields of physics — like quantum information and analog gravity — in order to produce something novel, or ‘cute,’ as he liked to say.”

“The Hawking process is one of the richest physical phenomena connecting seemingly unrelated fields of physics from the quantum theory to thermodynamics and relativity,” said Dimitrios Kranas, LSU graduate student. “Analog black holes came to add an extra flavor to the effect providing us, at the same time, with the exciting possibility of testing it in the laboratory. Our detailed numerical analysis allows us to probe new features of the Hawking process, helping us understand better the similarities and differences between astrophysical and analog black holes.”

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For metalloproteins to work properly, they must be paired with the correct metal ion — hemoglobin can only function with iron Yet, protein-metal binding is normally governed by a strict order, called the Irving-Williams Series, which dictates that copper ions should bind to proteins over other metals.

In other words, if a cell contained equal amounts of different metal ions, most cellular proteins and other components would bind to copper, clogging up cellular machinery in the process. This is why organisms spend considerable energy keeping very strict controls over how much free copper is present in cells.

Now researchers in the University of California San Diego’s Division of Physical Sciences have reported a new protein-design strategy to sidestep the Irving-Williams Series. The findings were published earlier this week in the journal Nature.

Professor of Chemistry and Biochemistry Akif Tezcan and postdoctoral scholar Tae Su Choi designed a flexible protein that selectively binds other metal ions over copper, paving the way for the design of novel functional proteins and metal sequestration agents. Choi and Tezcan discovered that selective binding to non-copper metals required the artificial protein to present a very specific combination of amino acids and geometries to discriminate against copper. This discovery required an uncommon design approach.

“Protein design typically involves trying to craft a discrete protein structure that can perform a certain function, such as catalysis. This approach is inherently deterministic and follows the sequence of one design-one structure-one function,” stated Tezcan. “Best case scenario, you obtain the structure and function that is designed. However, this approach doesn’t leave much room for the discovery of new design principles or unexpected outcomes, which are potentially more significant than what was originally planned.”

Tezcan and Choi took a probabilistic approach instead. At the outset, their designed protein wasn’t engineered to possess a singular structure that selectively binds to a certain type of metal. They created a flexible system that could arrange itself in multiple ways to bind different metal ions in different geometries. It was this flexibility that led them to an outcome they did not originally plan for.

“In analyzing these systems, we saw that proteins were binding to cobalt and nickel ions ahead of copper, which is not the natural order of things,” stated Choi. “We created an hypothesis and tested new variants. After extensive analysis, we realized we could construct a protein environment where copper was disfavored.”

“This is an example of designing a pathway rather that a target,” explained Tezcan. “I personally think that this is a more exciting way to go about the protein design problem. By incorporating an element of flexibility into the design, we leave open the possibility of different outcomes and new design principles we couldn’t have known beforehand.”

Research on selective metal binding and protein design has importance beyond a better understanding of the fundamentals of life. It can also lay the foundation for more efficient processes during environmental remediation, such as when certain metals need to be sequestered in contaminated water. Protein design is also a critical part of pharmaceutical research and development.

“We were intrigued by the question ‘Can we design proteins that can selectively bind to metals or have catalytic reactions in ways that evolution has not yet invented?'” said Choi. “Just because biology doesn’t do it, it doesn’t mean it’s not possible.”

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Materials provided by University of California – San Diego. Original written by Michelle Franklin. Note: Content may be edited for style and length.

‘We correctly diagnosed all patients with conditions that were already known, including Huntington’s disease, fragile X syndrome, hereditary cerebellar ataxias, myotonic dystrophies, myoclonic epilepsies, motor neuron disease and more,’ says Dr Ira Deveson, Head of Genomics Technologies at the Garvan Institute and senior author of the study.

The diseases covered by the test belong to a class of over 50 diseases caused by unusually-long repetitive DNA sequences in a person’s genes — known as ‘Short Tandem Repeat (STR) expansion disorders’.

‘They are often difficult to diagnose due to the complex symptoms that patients present with, the challenging nature of these repetitive sequences, and limitations of existing genetic testing methods,’ says Dr Deveson.

The study, published today in Science Advances, shows that the test is accurate, and allows the team to begin validations to make the test available in pathology services around the world.

A patient who participated in the study, John, first realised something wrong when he experienced unusual problems balancing during a ski lesson.

‘It was very worrying having symptoms that, over the years, increased in severity; from being active and mobile to not being able to walk without support. I had test after test for over ten years and absolutely no answers as to what was wrong,’ says John, who was eventually diagnosed with a rare genetic disease called CANVAS, which affects the brain.

‘It was reassuring to finally confirm my diagnosis genetically, and it’s exciting to know that, in the near future, others with these types of conditions will be able to get a diagnosis quicker than I did,’ he says.

‘For patients like John, the new test will be a game-changer, helping to end what can often be a taxing diagnostic odyssey,’ says Dr Kishore Kumar, a co-author of the study and clinical neurologist at the Concord Hospital.

Repeat expansion disorders can be passed on through families, can be life threatening and generally involve muscle and nerve damage, as well as other complications throughout the body.

Quicker, more-accurate diagnosis for patients avoids ‘diagnostic odyssey’

Current genetic testing for expansion disorders can be ‘hit and miss’, says Dr Kumar. ‘When patients present with symptoms, it can be difficult to tell which of these 50-plus genetic expansions they might have, so their doctor must decide which genes to test for based on the person’s symptoms and family history. If that test comes back negative, the patient is left without answers. This testing can go on for years without finding the genes implicated in their disease. We call this the ‘diagnostic odyssey’, and it can be quite stressful for patients and their families,’ he says.

‘This new test will completely revolutionise how we diagnose these diseases, since we can now test for all the disorders at once with a single DNA test and give a clear genetic diagnosis, helping patients avoid years of unnecessary muscle or nerve biopsies for diseases they don’t have, or risky treatments that suppress their immune system,’ says Dr Kumar.

Although repeat expansion disorders cannot be cured, a quicker diagnosis can help doctors identify and treat disease complications earlier, such as heart issues associated with Friedreich’s ataxia.

Scanning for known and novel diseases

Using a single DNA sample, usually extracted from blood, the test works by scanning a patient’s genome using a technology called Nanopore sequencing.

‘We’ve programmed the Nanopore device to hone in on the roughly 40 genes known to be involved in these disorders and to read through the long, repeated DNA sequences that cause disease,’ he says. ‘By unravelling the two strands of DNA and reading the repeated letter sequences (combinations of A, T, G or C), we can scan for abnormally long repeats within the patient’s genes, which are the hallmarks of disease.’

‘In the one test, we can search for every known disease-causing repeat expansion sequence, and potentially discover novel sequences likely to be involved in diseases that have not yet been described,’ says Dr Deveson.

Upscaling to wider use in the next five years

The Nanopore technology used in the test is smaller and cheaper than standard tests, which the team hopes will smooth its uptake into pathology labs. ‘With Nanopore, the gene sequencing device has been reduced from the size of a fridge to the size of a stapler, and costs around $1000, compared with hundreds of thousands needed for mainstream DNA sequencing technologies’ says Dr Deveson.

The team expects to see their new technology used in diagnostic practice within the next two to five years. One of the key steps towards that goal is to gain appropriate clinical accreditation for the method.

Once accredited, the test will also transform research into genetic diseases, says Dr Gina Ravenscroft, a co-author of the study and a researcher working on rare disease genetics at the Harry Perkins Institute of Medical Research.

‘Adult-onset genetic disorders haven’t received as much research attention as those that appear in early life,’ she says. ‘By finding more people with these rare adult-onset diseases, and those who may be pre-symptomatic, we’ll be able to learn more about a whole range of rare diseases through cohort studies, which would otherwise be hard to do.’

The work was supported predominantly by philanthropic funding from The Kinghorn Foundation.

Published today in Science Advances, the study found that the DNA-binding dye performed well in processed clinical tissue samples and generated high-quality images via superresolution fluorescence microscopy.

“My lab is focused on developing microscopy techniques to visualize the invisible,” said senior author Yang Liu, Ph.D., associate professor of medicine and bioengineering at the University of Pittsburgh. “We are one of the first groups to explore the capabilities of superresolution microscopy in the clinical realm. Previously, we improved its throughput and robustness for analysis of clinical cancer samples. Now, we have a DNA dye that is easy to use, which solves another big problem in bringing this technology to patient care.”

Inside the cell’s nucleus, DNA strands are wound around proteins like beads on a string. Pathologists routinely use traditional light microscopes to visualize disruption to this DNA-protein complex, or chromatin, as a marker of cancer or precancerous lesions.

“Although we know that chromatin is changed at the molecular scale during cancer development, we haven’t been able to clearly see what those changes are. This has bothered me for more than 10 years,” said Liu, who is also a member of the UPMC Hillman Cancer Center. “To improve cancer diagnosis, we need tools to visualize nuclear structure at much greater resolution.”

In 2014, the Nobel Prize-winning invention of superresolution fluorescence microscopy was a major step towards making Liu’s vision reality. A molecule of interest is labelled with a special fluorescent dye that flashes on and off like a blinking star. Unlike traditional fluorescence microscopy, which uses labels that glow constantly, this approach involves switching on only a subset of the labels at each moment. When several images are overlayed, the complete picture can be reconstructed — at a much higher resolution than previously possible.

Until now, the problem was that fluorescent dyes didn’t work well on DNA or in processed clinical cancer samples. So, Liu and her team formulated a new label called Hoechst-Cy5 by combining the DNA-binding molecule Cy5 and a fluorescent dye called Hoechst with ideal blinking properties for superresolution microscopy.

After showing that the new label produced higher resolution images than other dyes, the researchers compared colorectal tissue from normal, precancerous and cancerous lesions. In normal cells, chromatin is densely packed, especially at the edges of the nucleus. Condensed DNA glows brightly because a higher density of labels emits a stronger signal, while loosely packed chromatin produces a dimmer signal.

The images show that as cancer progresses, chromatin becomes less densely packed, and the compact structure at the nuclear border is severely disrupted. While these findings indicate that the new label can distinguish normal tissue from precancerous and cancerous lesions, Liu said that superresolution microscopy is unlikely to replace traditional microscopes for such routine clinical diagnoses. Instead, this technology could shine in risk stratification.

“Early-stage lesions can have very different clinical outcomes,” said Liu. “Some people develop cancer very quickly, and others stay at the precursor stage for a long time. Stratifying cancer risk is a major challenge in cancer prevention.”

To see if chromatin structure could hold clues about future cancer risk, Liu and her team evaluated patients with Lynch syndrome, a heritable condition that increases the risk of several cancer types, including colon cancer. They looked at non-cancerous colorectal tissue from healthy people without Lynch syndrome and Lynch patients with or without a personal history of cancer.

The differences were striking. In Lynch patients who previously had colon cancer, chromatin was much less condensed than in healthy samples, suggesting that chromatin disruption could be an early sign of cancer development — even in tissue that looks completely normal to pathologists.

For Lynch patients without a personal history of cancer, some will go on to develop cancer, while others will not.

“We see a much larger spread in this group, which is very interesting,” said Liu. “Some patients resemble healthy controls, and some are closer to Lynch patients who previously had cancer. We think that patients with more open chromatin are those who are more likely to develop cancer. We need to follow these patients over time to measure outcomes, but we’re pretty excited that chromatin disruption in normal cells could potentially predict cancer risk.”

In future work, Liu and her team are interested in examining chromatin structure in endometrial tissue from Lynch patients, who also have elevated risk of endometrial cancer. The researchers also received funding recently to look at sputum samples from smokers for early detection of lung cancer.

Other authors who contributed to this study were Jianquan Xu, Ph.D., Xuejiao Sun, M.S., Hongqiang Ma, Ph.D., Rhonda M. Brand, Ph.D., Douglas Hartman, M.D., and Randall E. Brand, M.D., all of Pitt; and Mingfeng Bai, Ph.D., and Kwangho Kim, Ph.D., both of Vanderbilt University.

This work was funded by the National Institutes of Health (R01CA254112, R33CA225494 and R01CA232593).

In The Physics Teacher, by AIP Publishing, scientists from Carleton College and the University of Colorado Boulder are helping to change this narrative by presenting discussions and activities on DEI as a fundamental and essential part of physics training beyond the introductory physics level.

“Diversity, equity, and inclusion are a part of being a physicist, just as much as knowing about quantum mechanics or using an oscilloscope,” said author Martha-Elizabeth Baylor.

The team created two separate approaches for DEI curriculum at the intermediate level in 30-person and 75- to 120-person classrooms. The former replaced one question on a weekly homework assignment with a reflection essay on a topic important to physicists. The latter included activities and discussions during a two-day unit on representation.

“On the whole, students respond positively to covering this material in a physics class,” said author Jessica Hoehn. “They are eager for these conversations.”

The reflection essays in the first approach were a small component of a larger “Practicing Professionalism” framework, which explored what physicists know, do, and care about. Meanwhile, the second approach tested students on the ideas within their DEI activities and discussions, just as it would with other course content.

Baylor said students began the term by writing themselves out of the definition of a physicist. However, that changed by the end of the class.

“Many students come to see that the physics community thinks about the things that they think about, the things they care about,” said Baylor. “They find that anybody can be a physicist. They just have to care about physics, choose to do physics, and choose that as part of their identity.”

For women in these classes in particular, a large theme emerged: Their feelings about being in physics were particular to the cultural environment in the U.S.

The authors believe instructors can look at each curriculum and design their own lessons that they are comfortable enacting. The individual reflection activities in the first approach may be an easier start for instructors who want to engage with students on an individual basis, rather than lead a class discussion.

The researchers recommend looking at their resources for ideas, then gathering feedback and iteratively improving the curriculum. They hope to help other instructors frame physics as a human endeavor.

“We’re doing this, because if you enter the physics community, you need to be able to engage intelligently and respectfully in these conversations,” said Baylor.

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More recently, however, cancer surgeons have discovered that CLND has the potential to cause more problems than it solves. In most cases, patients do better on immunotherapy alone than they do when their surgery involves removal of the lymph nodes, due to potential complications from lymph node surgery.

In a paper published in February in the Annals of Surgical Oncology, University of Colorado (CU) Cancer Center members Martin McCarter, MD, Camille Stewart, MD, Karl Lewis, MD, William Robinson, MD, Ana Gleisner, MD, PhD, and Rene Gonzalez, MD — along with CU School of Medicine resident Robert Torphy, MD, PhD — reviewed their patient data to determine if immunotherapy alone resulted in better outcomes than CLND.

“In the few years prior to immunotherapy being available, some surgical trials were done asking if regional node dissection by itself improves overall survival for the patients,” says McCarter, a professor of surgical oncology at the CU School of Medicine. “And the answer came back: no, it did not improve survival. That had been the standard forever, because we didn’t have other effective therapies, but once the definitive trials were done, we learned that CLND wasn’t helping, it wasn’t improving survival. Subsequent trials demonstrated that immunotherapy can improve survival in metastatic melanoma.”

Better outcomes with immunotherapy

For the study, Torphy, working with McCarter and the other researchers, looked at data on 90 patients who underwent sentinel lymph node biopsy (a procedure to determine if a skin melanoma has spread microscopically) only for stage III melanoma but did not undergo CLND. Of those patients, 56 received immunotherapy and 34 did not. Those who received immunotherapy had better rates of distant metastasis-free survival, meaning their cancer was less likely to come back.

“As treatments for melanoma have evolved, the standard of care may be evolving as well,” McCarter says. “This study took a look at the patients who had a sentinel lymph node biopsy, so we knew the patient had a positive melanoma metastasis to their regional node. Those folks historically used to go on and get the completion lymph node dissection, but recently, people started to forego doing that lymph node dissection, which did not improve survival, and instead moved directly to immunotherapy, which did improve survival in other clinical trials. We proved that this is acceptable, that we’re not causing more harm to patients by doing it, and that those who do go on to get the immunotherapy seem to benefit from it.”

The de-escalation movement

Forgoing CLND is part of a recent movement in cancer treatment known as de-escalation (or de-implementation) — giving patients only the surgery absolutely necessary to treat their immediate disease. It’s especially important when it comes to lymph node surgery, McCarter says, as on top of the risks inherent to all surgeries, CLND has a 20% to 30% risk of permanent lymphedema, potentially harmful tissue swelling caused by an accumulation of protein-rich fluid that’s usually drained through the body’s lymphatic system.

“If you could avoid that complication and not compromise a patient’s survival, that would be beneficial,” McCarter says. “That’s what we guessed was happening outside of definitive clinical trial evidence, and that’s what we were able to show. We know that we often overtreat patients, and this fits in that paradigm of finding ways to de-escalate unnecessary therapies, which has been done in breast cancer and other cancers as well.”

Changing course

The CU researchers hope the study begins to move the needle for cancer surgeons for whom CLND is still routine, despite the earlier studies showing that the additional surgery was not improving survival.

“Previous clinical trials with the use of adjuvant immunotherapy for melanoma had required a CLND,” McCarter says. “This study used real-world data from our stage III melanoma patients who were treated with immunotherapy without having a prior CLND.

“It takes years to change people’s practice patterns. I still have conversations with community surgeons who treat melanoma, asking me, ‘Should I be doing these regional node dissections?’ even though this data has been out for five to 10 years now,” McCarter continues. “They’re afraid to give up what they used to do, and they’re afraid that they are doing a disservice to the patients or not giving them the best chance, when in reality, our understanding of cancer biology has evolved. We now have effective immunotherapy, which is overcoming some of the limitations of surgery while improving outcomes.”