Category Archives: Cell Biology

Cell Biology

Impact of aldehydes on DNA damage and aging – EurekAlert

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Histones are crosslinked with DNA (histone-DPC) following formaldehyde exposure, leading to the malfunction of cellular processes such as transcription.

Credit: Reiko Matsushita

A team of researchers at Nagoya University in Japan has discovered that aldehydes are metabolic byproducts associated with premature aging. Published in Nature Cell Biology, their findings reveal insights into premature aging diseases and potential strategies to combat aging in healthy individuals such as controlling exposure to aldehyde-inducing substances including alcohol, pollution, and smoke.

A person's health can be harmed by aldehydes. However, the groups findings suggest these detrimental effects also include aging. The team who made this discovery included Yasuyoshi Oka, Yuka Nakazawa, Mayuko Shimada, and Tomoo Ogi of Nagoya University.

DNA damage is linked with aging phenotypes, said Oka. However, for the first time, we propose a relationship between aldehyde-derived DNA damage and premature aging.

The researchers hypothesized that there might be a link between aldehydes and aging since individuals with premature aging disorders, like AMeD syndrome, exhibit inadequate activity of enzymes, like ALDH2, that break down aldehydes.

For healthy individuals, ALDH2 is also important in our response to alcohol. When a person drinks wine or beer, the liver metabolizes the alcohol into aldehydes so it can be eliminated from the body. The activity of ALDH2 is important for converting the aldehydes into a non-toxic substance.

Aldehydes are harmful because they are highly reactive with DNA and proteins. In the body, they form DNA-protein crosslinks (DPCs) that block important enzymes in typical cell proliferation and maintenance processes, causing these processes to malfunction and the patient to age.

Focusing on DPCs caused by aldehyde, the scientists used a method called DPC-seq to investigate the link between aldehyde accumulation and DNA damage in premature-aging disease patients. In a series of experiments, the researchers discovered that the TCR complex, VCP/p97, and the proteasome are involved in the removal of formaldehyde-induced DPCs in actively transcribed regions. This was confirmed by a mouse model lacking both aldehyde clearance processes and the TCR pathway that showed worse AMeD syndrome symptoms.

These processes are important because they are related to the clearance of aldehydes. It suggests an association between premature aging diseases and aldehyde accumulation.

Professor Ogi is hopeful about the implications of their findings, stating: "By elucidating the mechanism by which DNA damage heals quickly, we have revealed part of the cause of genetic premature aging.

Our research opens up new avenues for understanding the underlying mechanisms of premature aging diseases and offers potential targets for therapeutic intervention, Oka said. By elucidating the role of aldehydes in DNA damage and aging, we are paving the way for future studies aimed at developing novel treatments and interventions."

He continued: The development of therapeutic drugs has not progressed because we have not fully understood the causes of AMeD syndrome and Cockayne syndrome. This study suggests that the patient's pathological condition is related to DPC derived from aldehydes generated within cells. These results are expected to help in the search for compounds that remove aldehydes, thus aiding in the formulation of therapeutic drug candidates.

This research has implications that extend beyond genetic diseases, as their findings suggest that aldehyde-induced DNA damage may play a role in the aging process in healthy individuals too. By pinpointing aldehydes as substances that contribute to aging, this study sheds light on the intricate connection between environmental factors and cellular aging. This may have significant implications for human health and lifespan.

Nature Cell Biology

Endogenous aldehyde-induced DNA-protein crosslinks are resolved by transcription-coupled repair

10-Apr-2024

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Impact of aldehydes on DNA damage and aging - EurekAlert

Cell Biology

Redefining Cell Biology: Nondestructive Genetic Insights With Raman Spectroscopy – SciTechDaily

A new method can track changes in live cell gene expression over extended periods of time. Based on Raman spectroscopy, the method doesnt harm cells and can be performed repeatedly. Credit: MIT News; iStock

A new MIT-developed method combines Raman spectroscopy with machine learning to noninvasively track gene expression in cells over time. This technique enables detailed study of cellular differentiation and has potential applications in cancer research, developmental biology, and diagnostics.

Sequencing all of the RNA in a cell can reveal a great deal of information about that cells function and what it is doing at a given point in time. However, the sequencing process destroys the cell, making it difficult to study ongoing changes in gene expression.

An alternative approach developed at MIT could enable researchers to track such changes over extended periods of time. The new method, which is based on a noninvasive imaging technique known as Raman spectroscopy, doesnt harm cells and can be performed repeatedly.

Using this technique, the researchers showed that they could monitor embryonic stem cells as they differentiated into several other cell types over several days. This technique could enable studies of long-term cellular processes such as cancer progression or embryonic development, and one day might be used for diagnostics for cancer and other diseases.

With Raman imaging, you can measure many more time points, which may be important for studying cancer biology, developmental biology, and a number of degenerative diseases, says Peter So, a professor of biological and mechanical engineering at MIT, director of MITs Laser Biomedical Research Center, and one of the authors of the paper.

Koseki Kobayashi-Kirschvink, a postdoc at MIT and the Broad Institute of Harvard and MIT, is the lead author of the study, which was published recently in the journal Nature Biotechnology. The papers senior authors are Tommaso Biancalani, a former Broad Institute scientist; Jian Shu, an assistant professor at Harvard Medical School and an associate member of the Broad Institute; and Aviv Regev, executive vice president at Genentech Research and Early Development, who is on leave from faculty positions at the Broad Institute and MITs Department of Biology.

Raman spectroscopy is a noninvasive technique that reveals the chemical composition of tissues or cells by shining near-infrared or visible light on them. MITs Laser Biomedical Research Center has been working on biomedical Raman spectroscopy since 1985, and recently, So and others in the center have developed Raman spectroscopy-based techniques that could be used to diagnose breast cancer or measure blood glucose.

However, Raman spectroscopy on its own is not sensitive enough to detect signals as small as changes in the levels of individual RNA molecules. To measure RNA levels, scientists typically use a technique called single-cell RNA sequencing, which can reveal the genes that are active within different types of cells in a tissue sample.

In this project, the MIT team sought to combine the advantages of single-cell RNA sequencing and Raman spectroscopy by training a computational model to translate Raman signals into RNA expression states.

RNA sequencing gives you extremely detailed information, but its destructive. Raman is noninvasive, but it doesnt tell you anything about RNA. So, the idea of this project was to use machine learning to combine the strength of both modalities, thereby allowing you to understand the dynamics of gene expression profiles at the single cell level over time, Kobayashi-Kirschvink says.

To generate data to train their model, the researchers treated mouse fibroblast cells, a type of skin cell, with factors that reprogram the cells to become pluripotent stem cells. During this process, cells can also transition into several other cell types, including neural and epithelial cells.

Using Raman spectroscopy, the researchers imaged the cells at 36 time points over 18 days as they differentiated. After each image was taken, the researchers analyzed each cell using single molecule fluorescence in situ hybridization (smFISH), which can be used to visualize specific RNA molecules within a cell. In this case, they looked for RNA molecules encoding nine different genes whose expression patterns vary between cell types.

This smFISH data can then act as a link between Raman imaging data and single-cell RNA sequencing data. To make that link, the researchers first trained a deep-learning model to predict the expression of those nine genes based on the Raman images obtained from those cells.

Then, they used a computational program called Tangram, previously developed at the Broad Institute, to link the smFISH gene expression patterns with entire genome profiles that they had obtained by performing single-cell RNA sequencing on the sample cells.

The researchers then combined those two computational models into one that they call Raman2RNA, which can predict individual cells entire genomic profiles based on Raman images of the cells.

The researchers tested their Raman2RNA algorithm by tracking mouse embryonic stem cells as they differentiated into different cell types. They took Raman images of the cells four times a day for three days, and used their computational model to predict the corresponding RNA expression profiles of each cell, which they confirmed by comparing it to RNA sequencing measurements.

Using this approach, the researchers were able to observe the transitions that occurred in individual cells as they differentiated from embryonic stem cells into more mature cell types. They also showed that they could track the genomic changes that occur as mouse fibroblasts are reprogrammed into induced pluripotent stem cells, over a two-week period.

Its a demonstration that optical imaging gives additional information that allows you to directly track the lineage of the cells and the evolution of their transcription, So says.

The researchers now plan to use this technique to study other types of cell populations that change over time, such as aging cells and cancerous cells. They are now working with cells grown in a lab dish, but in the future, they hope this approach could be developed as a potential diagnostic for use in patients.

One of the biggest advantages of Raman is that its a label-free method. Its a long way off, but there is potential for the human translation, which could not be done using the existing invasive techniques for measuring genomic profiles, says Jeon Woong Kang, an MIT research scientist who is also an author of the study.

Reference: Prediction of single-cell RNA expression profiles in live cells by Raman microscopy with Raman2RNA by Koseki J. Kobayashi-Kirschvink, Charles S. Comiter, Shreya Gaddam, Taylor Joren, Emanuelle I. Grody, Johain R. Ounadjela, Ke Zhang, Baoliang Ge, Jeon Woong Kang, Ramnik J. Xavier, Peter T. C. So, Tommaso Biancalani, Jian Shu and Aviv Regev, 10 January 2024, Nature Biotechnology. DOI: 10.1038/s41587-023-02082-2

The research was funded by the Japan Society for the Promotion of Science Postdoctoral Fellowship for Overseas Researchers, the Naito Foundation Overseas Postdoctoral Fellowship, the MathWorks Fellowship, the Helen Hay Whitney Foundation, the U.S. National Institutes of Health, the U.S. National Institute of Biomedical Imaging and Bioengineering, HubMap, the Howard Hughes Medical Institute, and the Klarman Cell Observatory.

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Redefining Cell Biology: Nondestructive Genetic Insights With Raman Spectroscopy - SciTechDaily

Cell Biology

Scientists Unravel the Unusual Cell Biology Behind Toxic Algal Blooms – SciTechDaily

The researchers were able to reconstruct the three-dimensional shape of the single chloroplast from several hundred images. Credit: University of Oldenburg / General and Molecular Microbiology group

What are the cellular mechanisms within a single-celled marine algae species responsible for triggering toxic algal blooms? A research group under the direction of microbiologist Prof. Dr. Ralf Rabus from the University of Oldenburg, Germany, has conducted first detailed analyses of the unusual cell biology of Prorocentrum cordatum, a globally widespread species of the dinoflagellates group, using both advanced microscopic and proteomics approaches.

As the team reports in the science journal Plant Physiology, the photosynthesis process in these microorganisms is organised in an unusual configuration which may help them to better adapt to the changing light conditions in the oceans. The results of the study could lead to an improved understanding of the incidence of harmful algal blooms, which may be becoming more frequent due to climate change.

Dinoflagellates are important organisms in both marine and freshwater ecosystems. These unicellular organisms make up a substantial proportion of free-living phytoplankton, which forms the basis of the food web in oceans and lakes. Some species, including Prorocentrum cordatum, can proliferate in warm, nutrient-rich waters and form harmful algal blooms.

Cross-section of a cell of the microalga Prorocentrum cordatum. The nucleus with the chromosomes is on the right. A single barrel-like chloroplast takes up 40 percent of the cell volume. Credit: University of Oldenburg / General and Molecular Microbiology group

We studied this organism because despite its environmental relevance its cell biology and metabolic physiology are still poorly understood, said Rabus. In addition to studying photosynthesis in the microalgae, the researchers also examined the structure of their cell nuclei and their response to heat stress in collaboration with teams from the Universities of Hanover, Braunschweig, and Munich and set out the findings in two other recently published papers.

Using a powerful scanning electron microscope with a focused ion beam at the Ludwig-Maximilians-Universitt Munich, the team headed by Rabus and lead author Jana Kalvelage from the Institute of Chemistry and Biology of the Marine Environment (ICBM) was able to reconstruct the three-dimensional architecture of the chloroplasts, where photosynthesis takes place. The scientists were able to generate around 600 image layers of a single algae cell and then combine the sections to create a three-dimensional, high-resolution spatial image of the oval-shaped single-celled organisms, which are generally around 10 to 20 thousandths of a millimeter long. The analysis revealed that Prorocentrum cordatum have only a single barrel-like chloroplast that takes up 40 percent of their cell volume.

Proteomic (protein) analyses then revealed marked differences between the photosynthetic apparatus of the microalgae and that of Arabidopsis thaliana, a well-studied model plant in genetics research. In both species, photosynthesis takes place in complex protein structures embedded in the chloroplasts extensive membrane system.

However, in Prorocentrum cordatum the team observed that the conversion of solar energy into biochemical energy takes place in a single large structure consisting of numerous proteins, known as a megacomplex, whereas in the chloroplasts of the plant species, the different steps of photosynthesis occur in spatially separated structures. The team also reported that P. cordatum uses a large number of different pigment-binding proteins to efficiently capture solar energy. This diversity is a special adaptation to the changing light conditions to which the organism is exposed in the oceans, Rabus explained.

Two other studies published last year highlight the microalgaes unusual biology: in the first a German-Australian team of which the ICBM researchers were also members found that the organisms have a very large genome with twice as many base pairs as in humans. The team also discovered that the algae change their metabolism and their rate of growth decelerates in response to heat stress. In a second publication, the team led by Rabus and Kalvelage described the cell nucleus in greater detail, reporting that P. cordatum has 62 chromosomes, an unusually high number that fills almost the entire cell nucleus. The function of a large proportion of the nuclear proteins that were identified by the researchers is currently unknown, the team observed.

We have investigated how this important microalgae functions at the molecular level. These findings form the basis for a better understanding of its role in the environment, Rabus stressed. Further investigations could provide answers to questions such as how the organisms metabolism reacts to other stress factors and why the species is able to adapt to such a wide range of environmental conditions, from those in the tropics to those in temperate climates, he explained.

Reference: Conspicuous chloroplast with light harvesting-photosystem I/II megacomplex in marine Prorocentrum cordatum by Jana Kalvelage, Lars Whlbrand, Jennifer Senkler, Julian Schumacher, Noah Ditz, Kai Bischof, Michael Winklhofer, Andreas Klingl, Hans-Peter Braun and Ralf Rabus, 08 February 2024, Plant Physiology. DOI: 10.1093/plphys/kiae052

The study was funded by the German Research Foundation.

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Scientists Unravel the Unusual Cell Biology Behind Toxic Algal Blooms - SciTechDaily

Cell Biology

Ancient retroviruses played a key role in the evolution of vertebrate brains – EurekAlert

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A myelinating oligodendrocyte(green)

Credit: Peggy Assinck, Altos Labs-Cambridge Institute of Science

Researchers report February 15 in the journal Cell that ancient viruses may be to thank for myelinand, by extension, our large, complex brains. The team found that a retrovirus-derived genetic element or retrotransposon is essential for myelin production in mammals, amphibians, and fish. The gene sequence, which they dubbed RetroMyelin, is likely a result of ancient viral infection, and comparisons of RetroMyelin in mammals, amphibians, and fish suggest that retroviral infection and genome-invasion events occurred separately in each of these groups.

Retroviruses were required for vertebrate evolution to take off, says senior author and neuroscientist Robin Franklin of Altos Labs-Cambridge Institute of Science. If we didnt have retroviruses sticking their sequences into the vertebrate genome, then myelination wouldnt have happened, and without myelination, the whole diversity of vertebrates as we know it would never have happened.

Myelin is a complex, fatty tissue that ensheathes vertebrate nerve axons. It enables rapid impulse conduction without needing to increase axonal diameter, which means nerves can be packed closer together. It also provides metabolic support to nerves, which means nerves can be longer. Myelin first appeared in the tree of life around the same time as jaws, and its importance in vertebrate evolution has long been recognized, but until now, it was unclear what molecular mechanisms triggered its appearance.

The researchers noticed RetroMyelins role in myelin production when they were examining the gene networks utilized by oligodendrocytes, the cells that produce myelin in the central nervous system. Specifically, the team was investigating the role of noncoding regions including retrotransposons in these gene networkssomething that hasnt previously been explored in the context of myelin biology.

Retrotransposons compose about 40% of our genomes, but nothing is known about how they might have helped animals acquire specific characteristics during evolution, says first author Tanay Ghosh, a computational biologist at Altos Labs-Cambridge Institute of Science. Our motivation was to know how these molecules are helping evolutionary processes, specifically in the context of myelination.

In rodents, the researchers found that the RNA transcript of RetroMyelin regulates the expression of myelin basic protein, one of the key components of myelin. When they experimentally inhibited RetroMyelin in oligodendrocytes and oligodendrocyte progenitor cells (the stem cells from which oligodendrocytes are derived), the cells could no longer produce myelin basic protein.

To examine whether RetroMyelin is present in other vertebrate species, the team searched for similar sequences within the genomes of jawed vertebrates, jawless vertebrates, and several invertebrate species. They identified analogous sequences in all other classes of jawed vertebrates (birds, fish, reptiles, and amphibians) but did not find a similar sequence in jawless vertebrates or invertebrates.

Theres been an evolutionary drive to make impulse conduction of our axons quicker because having quicker impulse conduction means you can catch things or flee from things more rapidly, says Franklin.

Next, the researchers wanted to know whether RetroMyelin was incorporated once into the ancestor of all jawed vertebrates or whether there were separate retroviral invasions in the different branches. To answer these questions, they constructed a phylogenetic tree from 22 jawed vertebrate species and compared their RetroMyelin sequences. The analysis revealed that RetroMyelin sequences were more similar within than between species, which suggests that RetroMyelin was acquired multiple times through the process of convergent evolution.

The team also showed that RetroMyelin plays a functional role in myelination in fish and amphibians. When they experimentally disrupted the RetroMyelin gene sequence in the fertilized eggs of zebrafish and frogs, they found that the developing fish and tadpoles produced significantly less myelin than usual.

The study highlights the importance of non-coding regions of the genome for physiology and evolution, the researchers say. Our findings open up a new avenue of research to explore how retroviruses are more generally involved in directing evolution, says Ghosh.

###

This research was supported by the Adelson Medical Research Foundation, the UK Multiple Sclerosis Society, the Wellcome Trust, and the Altos Labs-Cambridge Institute of Science.

Cell, Ghosh et al., A retroviral link to vertebrate myelination through retrotransposon RNA mediated control of myelin gene expression https://cell.com/cell/fulltext/S0092-8674(24)00013-8

Cell (@CellCellPress), the flagship journal of Cell Press, is a bimonthly journal that publishes findings of unusual significance in any area of experimental biology, including but not limited to cell biology; molecular biology; neuroscience; immunology; virology and microbiology; cancer; human genetics; systems biology; signaling; and disease mechanisms and therapeutics. Visit http://www.cell.com/cell. To receive Cell Press media alerts, contact press@cell.com.

Experimental study

Animals

A retroviral link to vertebrate myelination through retrotransposon RNA-mediated control of myelin gene expression

15-Feb-2024

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Ancient retroviruses played a key role in the evolution of vertebrate brains - EurekAlert

Cell Biology

Singapore scientists uncover a crucial link between cholesterol synthesis and cancer progression – EurekAlert

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A study led by scientists at Duke-NUS Medical School has identified the pivotal but previously unknown role of an enzyme, called FAXDC2, that is suppressed in cancers with hyperactive Wnt signalling. FAXDC2 regulates the production of cholesterol and cell signalling molecules, and its suppression causes abnormal cell growth. Restoring FAXDC2 function could potentially normalise cell behaviour in these cancers.

Credit: Babita Madan

SINGAPORE, 2 February 2024 Scientists led by a team at Duke-NUS Medical School have made a breakthrough in understanding the mechanisms that influence cancer cell growth and development. Publishing in theJournal of Clinical Investigation, the researchers illuminate the previously hidden role of a novel enzyme, called fatty acid hydroxylase domain containing 2 (FAXDC2), revealing its pivotal role in cholesterol synthesis and cancer progression.

The study details the cascade of molecular events beginning from the suppression of FAXDC2 to the disruption of normal cholesterol synthesis to altered cancer fates, highlighting a potential vulnerability in cancer cells that could be targeted for therapeutic intervention.

Our journey into the cellular drivers of cancer started with an exploration of the Wnt signalling pathway, a crucial player in cell growth and development, explainedAssistant Professor Babita Madan, first author of the study from Duke-NUSCancer & Stem Cell Biology(CSCB) Programme. It was during these studies that we stumbled upon the enzyme FAXDC2, which emerged as a central figure in controlling cancer and stem cells. Our discovery suggests that FAXDC2's activity, or its suppression, has profound implications for cellular growth and differentiation, painting a complex picture of the relationship between cancer biology and cholesterol synthesis.

The research began with a deep dive into the Wnt signalling pathway, known for its critical role in the regulation of both normal and cancer cell growth. Wnt signalling is a key signalling pathway that regulates growth and development and maintaining brain, skin, hair and intestinal cells. However, hyperactive Wnt signallingpresent in the cancer models employed in the studyimpairs cell differentiation and keeps the cancers in a stem cell-like state. These undifferentiated cancer stem cells proliferate rapidly and uncontrollably, promoting faster tumour progression, and are resistant to anti-cancer therapies.

Employing cutting-edge genomic technologies to unravel this complex biological process, the scientists attention was drawn to the enzyme FAXDC2 when they found it increased dramatically after pancreatic cancer models were treated with amade-in-Singapore Wnt inhibitor, ETC-159. In-depth analyses of colorectal cancer tissue samples corroborated this finding, showing a consistent pattern of FAXDC2 suppression and subsequent buildup of cholesterol precursors, including a building block of cholesterol called lophenol. The lower the FAXDC2 expression, the higher the level of lophenol.

FAXDC2 is a previously unknown enzyme that helps make cholesterol from the precursor lophenol. Importantly, how much FAXDC2 you have in your cells changes the amount of lophenol you have, explainedProfessor David Virshup, Director of the CSCB Programme and the senior author of the study. Lophenol appears to modulate the activity of the differentiation pathway and, therefore, we think it helps to keep cancer cells in a more stem cell-like state.

Prof Virshup emphasised the broader implications of these insights, saying, This study provides a fascinating glimpse into the molecular machinery of cancer cells. The role of FAXDC2 in regulating cholesterol synthesis opens new pathways for future therapies. Understanding these complex mechanisms paves the way for innovative approaches to combat cancer, emphasising the importance of cholesterol biosynthesis intermediates as important signalling molecules and potential drugs.

The discovery of FAXDC2s role in cancer biology marks just the beginning of a longer scientific journey. Further research is necessary to fully understand how the suppression of FAXDC2 and the resulting changes in cholesterol metabolism can be leveraged to develop new cancer therapies. The research team is keen on exploring the therapeutic potential of targeting FAXDC2 in cancer treatment, considering it as a possible avenue for the development of drugs that could inhibit cancer growth by modulating cholesterol synthesis pathways.

Additionally, the findings spur interest in preventative strategies that could mitigate the risk of cancer development by maintaining the balance of cholesterol precursors in the body. Understanding the triggers that lead to the suppression of FAXDC2 in cancer cells could pave the way for novel prevention methodologies, potentially offering new hope in the fight against cancer.

"These findings resonate with our unwavering commitment to improving patient care through pivotal discoveries, commentedProfessor Patrick Tan, Senior Vice-Dean for Research at Duke-NUS. The road ahead involves rigorous research and collaboration across various disciplines, all aimed at translating these fundamental insights into tangible medical breakthroughs that could one day transform cancer treatment and prevention strategies.

Journal of Clinical Investigation

Experimental study

Cells

The cholesterol biosynthesis enzyme FAXDC2 couples Wnt/-catenin to RTK/MAPK signaling

23-Jan-2024

Babita Madan and David Virshup have a financial interest in ETC-159.

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Singapore scientists uncover a crucial link between cholesterol synthesis and cancer progression - EurekAlert

Cell Biology

Scientists uncover a way to "hack" neurons’ internal clocks to speed up brain cell development – News-Medical.Net

The neurons that make up our brains and nervous systems mature slowly over many months. And while this may be beneficial from an evolutionary standpoint, the slow pace makes growing cells to study neurodegenerative and neurodevelopmental diseases -; like Parkinson's disease, Alzheimer's disease, and autism -; in the laboratory quite challenging.

Currently, nerve cells derived from human pluripotent stem cells take months to reach an adultlike state in the lab -; a timeline that mirrors the slow pace of human brain development. ("Pluripotent stem cells" have the potential to develop into many other kinds of cells.)

New research led by Memorial Sloan Kettering Cancer Center (MSK), however, has uncovered a way to "hack" the cells' internal clocks to speed up the process. And the work is shedding new light on how cells' developmental timetables are regulated.

"This slow pace of nerve cell development has been linked to humans' unique and complex cognitive abilities," saysLorenz Studer, MD, Director of MSK'sCenter for Stem Cell Biologyand the senior author of two recent studies published inNatureandNature Biotechnology."Previous research has suggested the presence of a 'clock' within cells that sets the pace of our neurons' development, but its biological nature had largely remained unknown -; until now."

Researchers, led by study first authorGabriele Ciceri, PhD, identified an epigenetic "barrier" in the stem cells that give rise to neural cells. ("Epigenetic changes" are ones that don't alter the DNA code.) This barrier acts as a brake on the development process and determines the rate at which the cells mature. By inhibiting the barrier, the scientists were able to speed up the neurons' development,they reported January 31 inNature.

While studying brain development in mice, I was struck by how neurons progress through a series of steps in a very precise schedule. But this schedule creates a big practical challenge when working with human neurons -; what takes hours and days in the mouse requires weeks and months in human cells."

Dr.Gabriele Ciceri,a senior research scientist in the Studer Lab at MSK'sSloan Kettering Institute

Furthermore, the team showed that this rate-setting epigenetic barrier is built into neural stem cells well before they differentiate into different types of neurons. They also found higher levels of the barrier in human neurons compared with mouse neurons, which may help explain differences in the pace of cell maturation in different species.

That such discoveries were made at a cancer center isn't as surprising as it might seem at first blush. The Studer Lab has long focused on harnessing advances in stem cell biology to develop new therapies for degenerative diseases and cancer -; both of which are strongly associated with aging.

Moreover,MSK has long been a leader in "basic science" research-; that is, science that seeks to build fundamental understanding of human biology.

About half of the National Institutes of Health (NIH) budget goes to funding basic science research. And the vast majority of drugs approved bythe Food and Drug Administration in recent years involved publicly funded basic research,according to the NIH.

"All of the major advances in cancer treatment in recent years -;immune checkpoint inhibitor therapy,CAR T cell therapy,cancer vaccines-; they're all rooted in basic research," saysJoan Massagu, PhD, Director of the Sloan Kettering Institute and MSK's Chief Scientific Officer. "Sometimes it can take years for the medical relevance of a particular discovery to become clear."

A second study, led by Studer Lab graduate studentsEmiliano HergenrederandAndrew Minottiand published January 2 inNature Biotechnology, identified a combination of four chemicals that together can promote neuronal maturation. Dubbed GENtoniK, the chemical cocktail both represses epigenetic factors that inhibit cell maturation and stimulates factors that promote it.

Along with helping to bring neurons to an adultlike state faster in the lab, the approach holds promise for other cell types, the researchers note.

Not only was GENtoniK shown to speed the maturation of cortical neurons (involved in cognitive functions) and spinal motor neurons (involved in movement), but the chemicals were also able to accelerate the development of several other types of cells derived from stem cells, including melanocytes (pigment cells) and pancreatic beta cells (endocrine cells).

"The generation of human neurons in a dish from stem cells provides a unique inroad into the study of brain health and disease," the journal editors note in aresearch briefingthat accompanied the study. "A major obstacle in the field arises from the fact that human neurons require many months to mature during development, making it difficult to recapitulate the process invitro. The authors provide a valuable research tool by developing a simple drug cocktail that speeds up the maturation timeframe."

The findings could be particularly helpful in modeling disorders like autism that involve problems with synaptic connectivity, Dr. Studer says.

Still, he notes, additional research is needed to develop models of neurodegenerative disorders that don't occur until very late in life, such as Parkinson's disease, which haslong been a focus of Studer's research.

"Typically, a person is 60 to 70 years old when the disease begins. No baby gets Parkinson's," he says. "So, for those diseases, we need to be able to put the cells not just into an adult state but into an aged-like state. That's something we're continuing to work on."

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Scientists uncover a way to "hack" neurons' internal clocks to speed up brain cell development - News-Medical.Net

Cell Biology

First atomic-scale ‘movie’ of microtubules under construction, a key process for cell division – EurekAlert

image:

scar Llorca is standing in the center; Marina Serna is first from the right.

Credit: Laura M. Lombarda/CNIO.

Researchers at the Centre for Genomic Regulation (CRG) , the Spanish National Cancer Research Center (CNIO) and the IBMB-CSIC solve a key problem in biology: how human cells build their microtubules

During cell division, microtubules function as nanometer-thick long ropes' inside cells that pull chromosomes apart so that each daughter cell receives a copy of the genetic material

The work published in Science lays the groundwork for future breakthroughs in the treatment of diseases ranging from cancer to neurodevelopmental disorders

Cells in the human body are constantly dividing. With each division the genetic information contained in the chromosomes is duplicated, and each daughter cell receives a complete copy of the genetic material. It is a sophisticated process, a clockwork mechanism that involves refined and fast changes within the cell. To make this possible, the cell relies on microtubules, tiny structures that are indeed tube-shaped. Understanding how they start forming is a long-standing question.

Now, for the first time, researchers at the Centre for Genomic Regulation (CRG), the Spanish National Cancer Research Center (CNIO) and the Spanish National Research Council (IBMB-CSIC) have succeeded in making the equivalent of a film showing how human cells initiate the construction of their microtubules.

The findings, published today in the journal Science, solve a problem brought up years ago and thus lay the groundwork for future breakthroughs in the treatment of diseases ranging from cancer to neurodevelopmental disorders.

Long ropes that pull chromosomes apart

scar Llorca, director of the Structural Biology Program at the CNIO and co-lead author of the study, describes what happens inside the cell when cell division begins: "The chromosomes, once they have duplicated genetic information, move to the center of the cell and the cell, in a very remarkable way, quickly sprouts from its two ends large tubes that hook the chromosomes and pull each of the copies towards the two poles of the cell. Only then is it possible to encapsulate a copy of all our genetic material in each daughter cell."

The structures that are launched "like long ropes that reach the chromosomes to divide them," explains Llorca, are the microtubules. "That's why we say that microtubules play a key role in cell division. We need to understand very well the mechanisms that trigger the formation of these microtubules, at the right place and at the right time."

They are also 'cellular highways'

Microtubules are tubes with a length of thousandths of a millimeter and a diameter of nanometers [millionths of a millimeter]. In addition to being key to cell division, they act as highways for moving cellular components between different areas of the cell. They are also structural elements that shape the cell itself, among other tasks. A good understanding of their formation has implications for multiple areas of biomedicine.

"Microtubules are critical components of cells. Here we capture the process in action inside human cells. Given the fundamental role of microtubules in cell biology, this could eventually lead to new therapeutic approaches for a wide range of disorders," explains ICREA Research Professor Thomas Surrey, CRG researcher and co-lead author of the paper in Science.

Molecular ring triggers microtubule formation

The high-resolution images now obtained answer a question that has been hanging in the air for years: how microtubule formation begins in the early stages of cell division.

We now know that it all starts when a complex structure made up of several proteins, and called g TuRC (pronounced 'gammaturc'), closes, forming a ring.

The shape of g TuRC, its three-dimensional structure, was discovered a few years ago, and it surprised researchers. It was expected that g TuRC would be a closed ring acting as a base mold on top of which the microtubule is built; but g TuRC appeared as an open ring. Its dimensions and shape were incompatible with those of a microtubule mold.

The new CRG and CNIO work unveils the mechanism by which g TuRC closes into a ring and effectively becomes a perfect mold, capable of launching microtubule formation. The closure of g TuRC occurs when the first molecular piece of a microtubule gets attached to it.

"That's the trick the cell uses to close g TuRC," explains Llorca. "As soon as this first brick enters, a region of g TuRC is able to hook it and, like a loop, acts as a latch that pulls the ring closed and launches the process."

Visualizing this process required purifying g TuRC from human cells and reproducing the microtubule initiation process in the test tube. The samples were observed with cryo-electron microscopes and artificial intelligence was used for data analysis.

One million frames in a movie at atomic scale

One of the challenges has been to deal with the high speed of the microtubule construction process. The CRG group succeeded in slowing it down in the laboratory, and also stopping the growth of microtubules in order to better analyze the initial stages of the process.

"We had to find conditions that allowed us to image over a million microtubules in the process of nucleation before they grow too long and obscure the action of -TuRC. We were able to achieve this using the molecular toolbox of our lab and then freeze the microtubule stubs in place," explains Cludia Brito, a postdoctoral researcher at the CRG and first author of the study.

The microtubules under construction were observed at the IBMB-CSIC's Electron Cryomicroscopy Platform, located at the Joint Electron Microscopy Center (JEMCA), inside the ALBA Synchrotron. "They were frozen in a thin layer of ice, preserving the natural shape of the molecules involved," explains Pablo Guerra, head of this Platform. Thats how the best experimental conditions for observing microtubules in formation were determined. The best frozen samples were then sent to BREM (Basque Resource for Electron Microscopy) for imaging, and the resulting images were transferred to Marina Serna and Oscar Llorca at the CNIO for analysis and determination of the three-dimensional structures at atomic resolution.

Artificial intelligence for assembly

In practice, having more than a million microtubules in different stages of growth is equivalent to having many frames of a movie in high resolution. You just have to arrange them in the right order to see the movie in progress. That task fell to the CNIO team, which used artificial intelligence techniques to complete it

Determining the three-dimensional structure of growing microtubules from microscope images has been extremely complex. We needed multiple digital image-processing tools," explains Marina Serna, CNIO researcher.

For Llorca, "the great challenge has been to analyze at high resolution the images of a dynamic process, where we were observing several stages at the same time. This has been possible thanks to the use of neural networks, which have allowed us to organize all this complexity.

The result are three-dimensional structures at atomic resolution that represent the different stages of how the construction of a microtubule begins, and how the -TuRC ring becomes the mold that launches the formation of microtubules.

Implications for health

As Llorca explains, "this finding is relevant because we have addressed a very basic mechanism of cell division, whose process in humans we did not know".

This basic knowledge is useful for learning how to correct errors in the functioning of microtubules, which are associated with cancer, neurodevelopmental disorders and other conditions ranging from respiratory problems to heart disease.

"Some of the drugs used today to treat cancer prevent the formation or dynamics of microtubules," says Llorca. "However, these drugs affect microtubules indiscriminately, both in cancer cells and in healthy cells, leading to side effects. Knowing in detail how microtubules are formed may contribute to the development of more targeted treatments that affect microtubule formation and allow progress in the treatment of cancer and other diseases."

Next step: understanding regulation

Thomas Surrey explains the next steps in understanding microtubules, which involve deciphering how microtubule formation is regulated: "The process of nucleation decides where the microtubules are in a cell and how many you have in the first place. It is likely that the conformational changes we observe are controlled by yet-to-be-found regulators in cells. Several candidates have been described in other studies, but their mechanism of action is unclear."

Further work, "clarifying how regulators bind to -TuRC and how they affect the conformational changes during nucleation, may transform our understanding of how microtubules work, and eventually offer alternative sites that one might want to target to prevent cancer cells from going through the cell cycle," Surrey concludes.

Experimental study

Cells

Transition of human -tubulin ring complex into a closed conformation during microtubule nucleation

1-Feb-2024

The authors declare that they have no competing interests

Originally posted here:
First atomic-scale 'movie' of microtubules under construction, a key process for cell division - EurekAlert

Cell Biology

Small RNAs take on the big task of helping skin wounds heal better and faster with minimal scarring – EurekAlert

image:

Deposition of laminin into wound bed contributes to blood vessel growth, which in turn, feeds normal skin regeneration. W - wound, BV - blood vessels.

Credit: The American Journal of Pathology

Philadelphia, February 1, 2024 New findings in The American Journal of Pathology, published by Elsevier, report that a class of small RNAs (microRNAs), microRNA-29, can restore normal skin structure rather than producing a wound closure by a connective tissue (scar). Any improvement of normal skin repair would benefit many patients affected by large-area or deep wounds prone to dysfunctional scarring.

Because the burden of non-healing wounds is so significant, it is sometimes called a silent pandemic. Worldwide, costs associated with wound care are expected to reach US$15 to 22 billion per year by 2024, exceeding the cost of managing obesity-related health problems in some parts of the world.

Lead investigator Svitlana Kurinna, PhD, Division of Cell Matrix Biology and Regenerative Medicine, FBMH, University of Manchester, explained, We had data showing that microRNAs can regulate skin growth. microRNAs do not code for proteins, so it wasnt clear exactly how such small molecules can make changes to the skin. We therefore studied underlying mechanisms that could be targeted to improve cutaneous wound healing.

The molecular events during early wound healing stages of inflammation and tissue formation have been well described using single cell sequencing and proteomic approaches. microRNAs are important factors in healing and may regulate functions in skin repair; however, the mechanisms underlying tissue remodeling are unclear. Scientists studying wound healing in microRNA-29 gene knockout transgenic mice suggest that the release of microRNA-29 targets promotes wound healing by regulating skin regeneration by binding long RNAs coding for structural protein laminin C2 (LAMC2) of the skin. This restores the normal skin structure rather than creating a connective tissue scar.

In the current study, researchers noted that wild type wounded mice healed quite well, but the skin of transgenic mice devoid of microRNA-29 regenerated even better. To understand the reasons, they conducted in-depth microscopic analysis of the transgenic wounds. They observed deposition of LAMC2usually found in one of the skin layers in wild micearound blood vessels inside the wounds of microRNA-29deficient transgenic mice. This observation indicates that microRNA-29 may be inhibiting the expression of LAMC2, and deletion in the transgenic mice relieved the inhibition, which resulted in faster wound healing.

Dr. Kurinna noted, These processes are likely mediated by microRNA-29 target microRNAs released upon removal of microRNA-29 to improve cell matrix adhesion. These results further suggest a link between LAMC2, improved angiogenesis, and re-epithelialization. We had expected a different change in skin regeneration; we thought the removal of microRNA-29 would help outer layers of the skin to grow faster, but it was the deep matrix of the wound that showed an improvement.

These findings in both mice and humans demonstrate the role of microRNA-29 in epidermal repair and suggest that the release of microRNA-29 targets, particularly LAMC2, promotes wound healing. The inhibition of microRNA-29 and/or overexpression of LAMC2 may be a new and effective strategy for improving wound healing.

Dr Kurinna concluded, Our findings are of particular interest because they show the mechanism to restore normal skin structure rather than a wound closure by a connective tissue (scar). Any improvement of normal skin repair would therefore help many patients affected by large-area or deep wounds prone to dysfunctional scarring.

American Journal Of Pathology

Observational study

Cells

Release of miR-29 Target Laminin C2 Improves Skin Repair

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Small RNAs take on the big task of helping skin wounds heal better and faster with minimal scarring - EurekAlert

Cell Biology

Shengjie Feng channels the powers of cryogenic electron microscopy – Newswise

BYLINE: Scott LaFee

Newswise Cryogenic electron microscopy (cryo-EM) is sciences view of the future, or more precisely, a look at life at the smallest of scales. The imaging technology uses the very tiny wavelengths of electrons (much shorter than the wavelengths of light) to make clear images of equally tiny things.

With cryo-EM, researchers can peer inside cells to create stop-action movies of proteins and other biomolecules jostling and connecting with each other while mitochondria and other organelles generate energy, assemble new molecules and transport cargo. It is biology in action, a revealing new way to parse the secrets of life that earned its developers the 2017 Nobel Prize in chemistry.

Shengjie Feng, Ph.D., who recently joined Sanford Burnham Prebys as an assistant professor, is an expert in how to leverage the powers of cryo-EM. My research is truly interdisciplinary, she says. I believe that the strong cryo-EM core facility, drug discovery, cancer research and neuroscience research at Sanford Burnham Prebys will play a crucial role in advancing my work.

Feng, who will be part of the Degenerative Diseases program, focuses on the creation and characteristics of ion channels, both in healthy cells and in disease conditions. Ion channels are protein molecules that span the cell membrane, allowing passage of ions (atoms or molecules with a net electric charge, such as sodium, calcium and potassium) from one side of the cell membrane to the other, from outside in or inside out. They are critical to cellular operations, including facilitating communications between cells. Feng has specifically studied ion channels in neural cells.

We perceive the outer world and construct our inner world through neural circuits in our brain, she says. While neurons are the fundamental unit of information integration, responsible for all cognitive behaviors, ion channels serve as the molecular foundation of the electrical signaling that facilitates cell-cell communication. The coordinated opening and closing of these molecules generate a continuous wave of electrical signals throughout the nervous system, which underlies our perception and cognition.

More broadly, Feng notes that ion channel dysfunction is associated with a wide range of diseases, including epilepsy, muscle tension, diabetes and various types of cancers. Approximately 15% of U.S. Food and Drug Administration-approved therapies currently target ion channels as key molecular players.

Yet, these channels remain poorly understood. Feng hopes that by using the visual superpowers of cryo-EM, she can better illuminate their underlying form and function, identifying new drug targets specifically associated with certain diseases.

I believe that one of the most significant obstacles in neuroscience lies in connecting the molecular level to the circuit level in order to accurately predict the behaviors of neurons and, ultimately, human behavior.

With advance in cryo-EM technology, we now have the ability to observe protein complexes in their natural environment at the atomic level. I am optimistic that cryo-EM can serve as the crucial tool needed to bridge the gap between molecular neuroscience and circuit and cognitive neuroscience.

Previously, Feng was a postdoctoral scholar at Howard Hughes Medical Institute and UC San Francisco, where she worked with biophysicist Yifan Cheng, M.D. and neuroscientist Lily Jan, Ph.D.

In Fengs most recent published work, she helped find a novel drug-binding groove in TMEM16F, an enzyme that moves lipids around in cell membranes that contributes to SARS-Cov-2-induced lung damage. The study is critical for understanding the mechanism of action and for designing drugs that target TMEM16F to potentially help COVID patients with severe symptoms.

Feng earned her Ph.D. in neuroscience at the Institute of Neuroscience, part of the Chinese Academy of Sciences, where she used mouse models to understand the mechanisms and functions of membrane proteins and ion channels during neural development and disease.

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Shengjie Feng channels the powers of cryogenic electron microscopy - Newswise

Cell Biology

Study pinpoints breast cancer cells-of-origi – EurekAlert

image:

Caption: Pre-cancerous breast tissue from a BRCA2 mutation carrier. Credit: Dr Bianca Capaldo, WEHI

Credit: Must credit Dr Bianca Capaldo, WEHI

Australian scientists have pinpointed likely cells-of-origin, the source cells that can grow into breast cancer, in women carrying a faulty BRCA2 gene who are at high risk of developing the disease.

The WEHI-led study also showed these cells have potential to be targeted with an existing cancer drug to delay tumour growth, in findings that may lead to future preventive treatments for the disease.

At a glance

Women with faulty BRCA2 genes are at a substantially higher risk of developing breast cancer, with 70% of carriers going on to develop the disease, which is often aggressive.

A milestone finding from a WEHI-led research study has pinpointed likely cells-of-origin that have the potential to develop into breast cancers in women carrying a faulty BRCA2 gene.

The scientists also uncovered a vulnerability in these cells that they successfully targeted with an existing cancer drug to delay tumour growth in the lab.

Abnormal cells

Women who inherit and carry a faulty BRCA2 gene have a substantially increased risk of developing breast cancer approximately 70% of carriers will develop the disease over their lifetime.

These cancers often occur at a young age and can be clinically aggressive. Early screening is encouraged and some women undertake preventive breast surgery (mastectomy) to reduce their breast cancer risk.

In a milestone finding published in Nature Cell Biology, researchers have discovered the likely cells-of-origin of cancer in BRCA2 carriers. By comparing cancer-free tissue samples from both carriers and non-carriers, they identified an aberrant population of cells that divide more quickly.

Study joint first author Dr Rachel Joyce said this perturbed cell population was found in the majority of tissue samples from women with a faulty BRCA2 gene.

Given they were found in most of the BRCA2 tissue samples from healthy females, we believe these may be the cells-of-origin that lead to future breast cancers in women that carry the BRCA2 mutation, Dr Joyce said.

Treatment targets

The aberrant cells in BRCA2 tissue, a subset of breast ductal cells called luminal progenitor cells, stood out to the scientific team because they displayed altered protein production, which is critical for the correct growth and functioning of tissues in our bodies.

These changes may also make the cells more vulnerable to certain therapies aimed at preventing or delaying breast cancer development, said study joint first author Dr Rosa Pascual.

Lead author Professor Jane Visvader said the team developed a pre-clinical BRCA2 model that showed similar alterations in the ductal cells, and targeted them with the existing cancer drug everolimus, which is approved to treat patients with relapsed breast cancer.

Through pinpointing this vulnerability in protein production, we were able to show that pre-treatment with this drug delayed the formation of tumours in the pre-clinical model, said Prof Visvader, joint head of the ACRF Cancer Biology and Stem Cells Division and the Breast Cancer Laboratory at WEHI.

This raises the possibility that targeting specific aspects of protein production in this way could represent a new breast cancer prevention strategy for women with a faulty BRCA2 gene.

Towards prevention

The findings are an important first step towards the goal of preventative treatments for breast cancer in BRCA2-mutation carriers.

Study author and cancer clinician, Professor Geoff Lindeman said that while the findings were exciting, more work was needed before they could be applied in the clinic.

While everolimus did delay tumour development in the lab, this drug can have side-effects, which might limit its capacity to be used as a preventative treatment," said Prof Lindeman, joint head of the ACRF Cancer Biology and Stem Cells Division at WEHI, and a medical oncologist at the Royal Melbourne Hospital and Peter MacCallum Cancer Centre.

Our team want to further explore which specific parts of protein processing are dysregulated, and use this information to develop more selective and tolerable preventative treatments.

Theres still a way to go, but were a big step closer.

A few years ago, we identified the likely cells-of-origin for breast cancer in females carrying a fault in the BRCA1 gene, which is also associated with a high risk of developing breast cancer. That research has since led to an international breast cancer prevention study (BRCA-P).

We hope that our new findings will now inform future treatment and prevention for women with a faulty BRCA2 gene.

The study, Identification of aberrant luminal progenitors and mTORC1 as a potential breast cancer prevention target in BRCA2 mutation carriers, is published in Nature Cell Biology (DOI: 10.1038/s41556-023-01315-5).

The research was carried out on breast tissue samples kindly donated by women undergoing breast surgery, with assistance from the Victorian Cancer Biobank (funded by the Victorian Government) and the Kathleen Cuningham Foundation Consortium for research into Familial Breast cancer. The research was supported by the National Health and Medical Research Council, Breast Cancer Research Foundation, the National Breast Cancer Foundation, The Medical Research Future Fund, the Two Sisters Foundation and the Heine Family.

M: +61 475 751 811 E:communications@wehi.edu.au

About WEHI (Walter and Eliza Hall Institute of Medical Research) WEHI is where the worlds brightest minds collaborate and innovate to make life-changing scientific discoveries that help people live healthier for longer. Our medical researchers have been serving the community for more than 100 years, making transformative discoveries in cancers, infectious and immune diseases, developmental disorders, and healthy ageing. WEHI brings together diverse and creative people with different experience and expertise to solve some of the worlds most complex health problems. With partners across science, health, government, industry, and philanthropy, we are committed to long-term discovery, collaboration, and translation. At WEHI, we are brighter together. Find out more at http://www.wehi.edu.au

Nature Cell Biology

Observational study

Cells

Identification of aberrant luminal progenitors and mTORC1 as a potential breast cancer prevention target in BRCA2 mutation carriers

12-Jan-2024

Disclaimer: AAAS and EurekAlert! are not responsible for the accuracy of news releases posted to EurekAlert! by contributing institutions or for the use of any information through the EurekAlert system.

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Study pinpoints breast cancer cells-of-origi - EurekAlert