TL;DR
- Cancer cells and leukocytes are able to move through tissue and organs quickly. However, it is not fully understood how these mobile cells manage to travel and survive far away from their place of origin. Scientists have now revealed a general biomechanical principle of cell migration that allows cells to move freely, especially in rough terrain.
- Using a “barcoding” technique and CRISPR gene-editing technology, CARLIN can identify different cell types as they emerge and what genes each is turning on. Details about CARLIN emerged in the journal Cell, in an article titled, “An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.”
- Mutations in white blood cells can contribute to abnormal immune profile after hematopoietic stem cell transplantation.
- Potentially cancerous cells kept in check by competitive neighbours, study of oesophagus finds.
- Microneedles made of silk-based material can target plant tissues for delivery of micronutrients, hormones, or genes. A new method developed by engineers may offer a starting point for delivering life-saving treatments to plants ravaged by diseases.
- Unlike humans and other mammals, the skeletons of sharks, skates, and rays are made entirely of cartilage and they continue to grow that cartilage throughout adulthood. New research finds that adult skates go one step further than cartilage growth: They can also spontaneously repair injured cartilage. This is the first known example of adult cartilage repair in a research organism. The team also found that newly healed skate cartilage did not form scar tissue.
- Biomedical engineers at Duke University say they have devised a new imaging device capable of measuring both the thickness and texture of the various layers of the retina at the back of the eye. The advance could be used to detect a biomarker of Alzheimer’s disease, potentially offering a widespread early warning system for the disease, according to the team.
- Researchers have developed a first-of-its-kind roadmap of how human skeletal muscle develops, including the formation of muscle stem cells.
- Gene drive organisms (GDOs) have been suggested as an approach to solve some of the most pressing environmental and public health issues. Currently, it remains unclear what kind of regulations are to be used to cover the potential risks. Scientists have evaluated the options for an operational risk assessment of GDOs before their release into environments across the EU.
- Pneumococcus experts at the University of Alabama at Birmingham describe “A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus” in mBio, a newly-found capsule — the 100th to be identified since the pathogen was first discovered in the late 19th century.
- The team of investigators led by scientists at UT Southwestern has uncovered that the malaria parasite is driven by its own inherent clock. This discovery overturns decades of conventional wisdom about malaria, as the prevailing theory has been that the parasite takes its cues from its animal hosts.
- Researchers in Brazil have identified a group of co-expressed genes that are dysregulated in induced pluripotent stem cell (iPSC)-derived neuronal cells from patients with autism spectrum disorder (ASD), and which could potentially be used as a biomarker or even therapeutic target for the neurodevelopmental disorder.
- A 15-year Nature Genetics study has revealed 32 new genetic variants that appear to alter breast cancer risk.
- Good news for COVID-19 vaccine: immune system shows robust response to SARS-CoV-2.
- COVID-19 drives CRISPR diagnostics.
- Smart AI use could benefit Biopharma.
- And more!
Overview
Genetic technology is defined as the term which includes a range of activities concerned with the understanding of gene expression, advantages of natural genetic variation, modifying genes and transferring genes to new hosts. Genes are found in all living organisms and are transferred from one generation to the next. Gene technology encompasses several techniques including marker-assisted breeding, RNAi and genetic modification. Only some gene technologies produce genetically modified organisms.
Modern genetic technologies like genome editing would not be possible without all the previous generations of genetic technologies that have enabled scientists to discover what genes are, what they do and how DNA can be modified to add, remove or replace genes. You can find major genetic technologies development milestones via the link.
Gene Technology Market
- The valuation of the genetic engineering market is projected to escalate to USD 6.90 MN by the end of 2027.
- Global Genetic Engineering Market is projected to grow at 12.48% CAGR during the assessment period (2017–2027).
- North America holds the largest share in the global genetic engineering market, followed by Europe and the Asia Pacific, respectively.
- Merck KGaA (Germany), Thermo Fisher Scientific Inc. (US), Horizon Discovery Group Plc. (UK), Transposagen Biopharmaceuticals Inc. (US), Genscript Biotech Corporation (US), New England Biolabs (US), Lonza Group Ltd. (Switzerland), Inc. (US), and Integrated DNA Technologies, Inc. (US), and Origene Technologies, Inc. (US), are some of the major players operating in the genetic engineering market.
Another research provider, MarketsandMarkets, forecasts the genome editing, genome engineering market to grow from USD 3.19 billion in 2017 to USD 6.28 billion by 2022, at a compounded annual growth rate (CAGR) of 14.5% during the forecast period. The key factors propelling market growth are rising government funding and growth in the number of genomics projects, high prevalence of infectious diseases (like COVID-19) and cancer, technological advancements, increasing production of genetically modified (GM) crops, and growing application areas of genomics.
Recent Market-Players’ Developments:
- In 2019, Merck signed a license agreement with Evotec SE. This agreement will enable Evotec access to Merck’s foundational CRISPR intellectual property.
- In 2018, Thermo Fisher Scientific, Inc. expanded its Genome Editing IP Portfolio.
- In 2018, Horizon Discovery launched Edit-R CRISPRa arrayed crRNA (CRISPR RNA) libraries, an addition to its CRISPR activation (CRISPRa) reagent platform.
Genetics News & Researches
Potentially cancerous cells kept in check by competitive neighbours, study of oesophagus finds:
A 15-year Nature Genetics study has revealed 32 new genetic variants that appear to alter breast cancer risk: 15 were linked with at least one tumour feature: 7 were associated with ER status, 7 to the tumour grade, 4 to HER2 status and 2 to PR status.
Cellular locomotion using environmental topography
by Anne Reversat, Florian Gaertner, Jack Merrin, Julian Stopp, Saren Tasciyan, Juan Aguilera, Ingrid de Vries, Robert Hauschild, Miroslav Hons, Matthieu Piel, Andrew Callan-Jones, Raphael Voituriez & Michael Sixt in Nature
Whilst the whole world is in lockdown during the current Corona crisis, certain cells within our bodies are still travelling long-distance: while this happens when you develop pneumonia, any ordinary cut on your finger will also trigger white blood cells — aka leukocytes — to instantly move out of your blood vessels into the site of inflammation. Similarly, cancer cells, which can originate in any tissue or organ, can also spread and reproduce far away from their place of origin. The result: a metastasis.
Usually, every cell within the organism binds to its surrounding via specific adhesion receptors that are present on its plasma membrane. As universal “glue” between cells and their surroundings, these adhesion receptors, or integrins, either stabilize a cell if it needs to remain immobile, or serve as anchors when the cell climbs through the tissue. But how can certain types of cells such as white blood cells flexibly crawl through different tissues, although these tissues are composed of very distinct molecules that do not necessarily match the adhesion receptors?
The mystery has been solved in a recent Nature study by the group of Michael Sixt at the Institute of Science and Technology Austria (IST Austria) and collaborators from France. Combining experiments with physical models, the scientists describe a new mechanism of cell locomotion that works completely independent of a cell specifically binding to the extracellular environment. Instead, the cells use the geometry of the environment to propel themselves.
In their experiments, the biologists used different types of leukocytes from which they genetically eliminated the function of integrins to interrupt the binding between the cells and their extracellular environment. While integrins are essential for the survival and movement of almost all cell types, the IST Austria scientists had discovered in a previous study that leukocytes can move and survive without integrins. The same turned out to be true for some cancer cells.
To analyze the locomotion mechanism that allows cells to migrate in the absence of adhesion, the scientists focused on the geometry of the environment rather than its molecular composition. They engineered tiny cell-sized “microfluidic” channels with different wall geometries: from completely smooth to rough or serrated texture. They then let the cells migrate through these channels to observe that the integrin-deprived cells were not able to move forward when the walls were smooth and parallel. “The cells were ‘running on the spot’ — just like a car tire would spin on icy grounds,” says Anne Reversat, first author of the study and former IST Austria postdoc, who is now doing research at the University of Liverpool. “However, when the walls were textured with bumps, the cells could efficiently migrate without integrins. Cells that still carried their integrins could equally migrate in both rough textured and smooth channels.”
By looking closer experimentally and theoretically at the biomechanics of such “off-road” cell movement, Reversat et al. uncovered the unifying mechanical theme that underlies both modes of locomotion: Actin — the filamentous building material of the cell’s cytoskeleton — flows from the front of the cell to the tail end. This “retrograde actin flow” is the force within the cell that, once coupled to the environment, drives the cell body forward. Force-coupling can happen via integrins that penetrate the plasma membrane and thereby connect the intracellular actin with the extracellular substrate.
As the scientists found, however, actin cannot only couple through integrins; it can also couple without any transmembrane receptors. Reversat: “The retrograde flow generates intracellular shear forces that push against the channel walls whenever there is a bump. If the walls are parallel, or the bumps are too far apart, this does not work. Another way to see this is that the cell propels itself by changing its shape over time. After all, leukocytes are amoeboid cells — ‘amoibos’ being the Greek word for ‘changing’. As the fine structure of tissues is geometrically very complex, amoeboid cells can always rely on this mode of locomotion. This makes them enormously adaptable. Essentially, they can go everywhere.”
An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells
Using a “barcoding” technique and CRISPR gene-editing technology, CARLIN can identify different cell types as they emerge and what genes each is turning on
Every organism has its own family tree. And like any family tree, an organism’s family tree is more interesting if it’s both complete and richly detailed. That is, each member of the family tree should be displayed in their proper place along with some biographical information. In the case of an organism — a mouse, for example — the family tree’s members are individual cells, and the biographical information consists of gene expression profiles.
If comprehensive whole-organism family trees could be assembled, researchers would learn a lot about development, aging, and disease. Unfortunately, family trees that trace tissue or organism development have been limited to small groups of cells or rendered vaguely suspect, due to distortions cause by intrusive cell assessment techniques.
The good news is that a new technology has been developed that can serve as a sort of ancestry.com for an organism’s cells. That is, it promises to couple cell ancestry information with detailed molecular readouts, such as transcriptional signatures.
The technology, which is called CRISPR Array Repair Lineage tracing (CARLIN), was developed by scientists at the Stem Cell Research program at Boston Children’s Hospital and Dana-Farber Cancer Institute/Harvard Medical School. It can be used to track every cell in the body, from the embryonic stage until adulthood.
Details about CARLIN emerged in the journal Cell, in an article titled, “An Engineered CRISPR-Cas9 Mouse Line for Simultaneous Readout of Lineage Histories and Gene Expression Profiles in Single Cells.”
“This model exploits CRISPR technology to generate up to 44,000 transcribed barcodes in an inducible fashion at any point during development or adulthood, is compatible with sequential barcoding, and is fully genetically defined,” the article’s authors wrote. “We have used CARLIN to identify intrinsic biases in the activity of fetal liver hematopoietic stem cell (HSC) clones and to uncover a previously unappreciated clonal bottleneck in the response of HSCs to injury.”
“The dream that many developmental biologists have had for decades is a way to reconstruct every single cell lineage, cell by cell, as an embryo develops, or as a tissue is built up,” said Fernando Camargo, PhD, a senior investigator in the Stem Cell Research program and co-senior author on the paper with Sahand Hormoz, PhD, researcher, Dana-Farber Cancer Institute and assistant professor of systems biology, Harvard Medical School. “We could use this mouse model to follow its entire development.”
Camargo, Hormoz, and co-first authors for their respective labs — Sarah Bowling, PhD, and Duluxan Sritharan — created the mouse model using a method they call CRISPR Array Repair Lineage tracing, or CARLIN. The model can reveal cell lineages — the “family tree” in which parent cells create different types of daughter cells — as well as what genes are turned on or off in every cell over time.
Previously, scientists have only been able to trace small groups of cells in mice using dyes or fluorescent markers. Tags or barcodes have also been used, but previous approaches required prior knowledge of markers to isolate different cell types, or required time-consuming extraction and manipulation of cells, which could affect their properties. The advent of CRISPR has enabled researchers to barcode cells without perturbing the cells and to follow the lineage of thousands of cells simultaneously.
Using an inducible form of CRISPR, the researchers can create up to 44,000 different identifying barcodes at any time point in a mouse’s lifespan. The scientists can then read out the barcodes using another technology called single-cell RNA sequencing, enabling collection of information on thousands of genes that are turned on in each barcoded cell. This, in turn, provides information about the cells’ identity and function.
As a test case, the researchers used the new system to reveal unknown aspects of blood development during embryonic development, and to observe the dynamics of blood replenishment after chemotherapy in adult mice.
But the researchers believe their system could also be used to understand the changes in cellular lineage trees during disease and aging. Additionally, the system could be used to record the response to environmental stimuli like pathogen exposure and nutrient intake.
“Being able to create single-cell lineage maps of mammalian tissues is unprecedented,” said Camargo, who is also a member of the Harvard Stem Cell Institute. “Besides its many applications to studying developmental biology, our model will provide important insight on the cell types and hierarchies that are affected as organisms respond to injury and disease.”
Somatic mTOR mutation in clonally expanded T lymphocytes associated with chronic graft versus host disease
by Daehong Kim, Giljun Park, Jani Huuhtanen, Sofie Lundgren, Rajiv K. Khajuria, Ana M. Hurtado, Cecilia Muñoz-Calleja, Laura Cardeñoso, Valle Gómez-García de Soria, Tzu Hua Chen-Liang, Samuli Eldfors, Pekka Ellonen, Sari Hannula, Matti Kankainen, Oscar Bruck, Anna Kreutzman, Urpu Salmenniemi, Tapio Lönnberg, Andrés Jerez, Maija Itälä-Remes, Mikko Myllymäki, Mikko A. I. Keränen, Satu Mustjoki in Nature Communications
Mutations in white blood cells can contribute to abnormal immune profile after hematopoietic stem cell transplantation
Graft-versus-host disease (GvHD) is a potentially life-threatening medical condition that is common after allogeneic hematopoietic stem cell transplantation, the only curative treatment for various types of leukemias. In GvHD, white blood cells from transplant donor recognize recipient cells as non-self and attack recipient tissues. Understanding how these donor white blood cells remain active against recipient cells can pave the way for novel treatment strategies in GvHD.
A research project led by Professor Satu Mustjoki at the University of Helsinki investigated the role of T cell mutations in GvHD. Somatic or so-called acquired mutations during lifetime are common in cancer cells, but little is known about their existence and significance in other cells, such as cells in the body’s defense system.
Published in the journal Nature Communications, the study first identified an index chronic GvHD patient with an activating somatic mutation in a gene called mTOR, which regulates cell growth and cell survival.
The authors then screened an international cohort of 135 GvHD patients and 54 healthy blood donors. By using next generation sequencing, the scientists found that 2.2% of chronic GvHD patients, but none of the healthy blood donors, harbored a mutation in mTOR.
“What makes our finding particularly significant is that the mutation now found was recurrent, meaning that the same mutation was found in several patients with chronic GvHD,” says professor Satu Mustjoki.
“Our previous studies in rheumatoid arthritis had shown that acquired mutations could be found in T cells, but in these studies, the mutations had been isolated and the same mutations had not been found in more than one patient.”
Using single-cell RNA sequencing and T cell receptor sequencing on samples collected from the index patient, researchers found that the mTOR mutated CD4+ T cell clone expanded during the course of GvHD despite immunosuppressive treatment, suggesting the mutation contributed to the disease pathogenesis.
In addition, it was found that the mutation was located in so-called cytotoxic T cells and these cells were able to damage the body’s own cells. Researchers also investigated the mTOR mutation in more detail by introducing it into a human cell line. The activating mTOR mutation promoted cell proliferation and cell survival.
The researchers performed a high-throughput drug screen with 527 drugs to identify potential targeted therapies. The index patients’ CD4+ T cells were sensitive to a specific class of drugs called HSP90 inhibitors, suggesting that these drugs could be used to treat GvHD in the future.
“Our study helps to understand the mechanisms of activation of the immune system in GvHD. Although several different drug combinations have been tried in the treatment of GvHD, using our results, it is possible to find individualized treatments for patients,” says doctoral candidate Daehong Kim from the University of Helsinki.
Engineers develop precision injection system for plants
Microneedles made of silk-based material can target plant tissues for delivery of micronutrients, hormones, or genes. A new method developed by engineers may offer a starting point for delivering life-saving treatments to plants ravaged by diseases.
These diseases are difficult to detect early and to treat, given the lack of precision tools to access plant vasculature to treat pathogens and to sample biomarkers. The MIT team decided to take some of the principles involved in precision medicine for humans and adapt them to develop plant-specific biomaterials and drug-delivery devices.
The method uses an array of microneedles made of a silk-based biomaterial to deliver nutrients, drugs, or other molecules to specific parts of the plant. The findings are described in the journal Advanced Science, in a paper by MIT professors Benedetto Marelli and Jing-Ke-Weng, graduate student Yunteng Cao, postdoc Eugene Lim at MIT, and postdoc Menglong Xu at the Whitehead Institute for Biomedical Research.
The microneedles, which the researchers call phytoinjectors, can be made in a variety of sizes and shapes, and can deliver material specifically to a plant’s roots, stems, or leaves, or into its xylem (the vascular tissue involved in water transportation from roots to canopy) or phloem (the vascular tissue that circulates metabolites throughout the plant). In lab tests, the team used tomato and tobacco plants, but the system could be adapted to almost any crop, they say. The microneedles can not only deliver targeted payloads of molecules into the plant, but they can also be used to take samples from the plants for lab analysis.
The work started in response to a request from the U.S. Department of Agriculture for ideas on how to address the citrus greening crisis, which is threatening the collapse of a $9 billion industry, Marelli says. The disease is spread by an insect called the Asian citrus psyllid that carries a bacterium into the plant. There is as yet no cure for it, and millions of acres of U.S. orchards have already been devastated. In response, Marelli’s lab swung into gear to develop the novel microneedle technology, led by Cao as his thesis project.
The disease infects the phloem of the whole plant, including roots, which are very difficult to reach with any conventional treatment, Marelli explains. Most pesticides are simply sprayed or painted onto a plant’s leaves or stems, and little if any penetrates to the root system. Such treatments may appear to work for a short while, but then the bacteria bounce back and do their damage. What is needed is something that can target the phloem circulating through a plant’s tissues, which could carry an antibacterial compound down into the roots. That’s just what some version of the new microneedles could potentially accomplish, he says.
“We wanted to solve the technical problem of how you can have a precise access to the plant vasculature,” Cao adds. This would allow researchers to inject pesticides, for example, that would be transported between the root system and the leaves. Present approaches use “needles that are very large and very invasive, and that results in damaging the plant,” he says. To find a substitute, they built on previous work that had produced microneedles using silk-based material for injecting human vaccines.
“We found that adaptations of a material designed for drug delivery in humans to plants was not straightforward, due to differences not only in tissue vasculature, but also in fluid composition,” Lim says.
The microneedles designed for human use were intended to biodegrade naturally in the body’s moisture, but plants have far less available water, so the material didn’t dissolve and was not useful for delivering the pesticide or other macromolecules into the phloem. The researchers had to design a new material, but they decided to stick with silk as its basis. That’s because of silk’s strength, its inertness in plants (preventing undesirable side effects), and the fact that it degrades into tiny particles that don’t risk clogging the plant’s internal vasculature systems.
They used biotechnology tools to increase silk’s hydrophilicity (making it attract water), while keeping the material strong enough to penetrate the plant’s epidermis and degradable enough to then get out of the way.
Sure enough, they tested the material on their lab tomato and tobacco plants, and were able to observe injected materials, in this case fluorescent molecules, moving all they way through the plant, from roots to leaves.
“We think this is a new tool that can be used by plant biologists and bioengineers to better understand transport phenomena in plants,” Cao says. In addition, it can be used “to deliver payloads into plants, and this can solve several problems. For example, you can think about delivering micronutrients, or you can think about delivering genes, to change the gene expression of the plant or to basically engineer a plant.”
“Now, the interests of the lab for the phytoinjectors have expanded beyond antibiotic delivery to genetic engineering and point-of-care diagnostics,” Lim adds.
For example, in their experiments with tobacco plants, they were able to inject an organism called Agrobacterium to alter the plant’s DNA — a typical bioengineering tool, but delivered in a new and precise way.
So far, this is a lab technique using precision equipment, so in its present form it would not be useful for agricultural-scale applications, but the hope is that it can be used, for example, to bioengineer disease-resistant varieties of important crop plants. The team has also done tests using a modified toy dart gun mounted to a small drone, which was able to fire microneedles into plants in the field. Ultimately, such a process might be automated using autonomous vehicles, Marelli says, for agricultural-scale use.
A Human Skeletal Muscle Atlas Identifies the Trajectories of Stem and Progenitor Cells across Development and from Human Pluripotent Stem Cells
An interdisciplinary team of researchers at the Eli and Edythe Broad Center for Regenerative Medicine and Stem Cell Research at UCLA has developed a first-of-its-kind roadmap of how human skeletal muscle develops, including the formation of muscle stem cells.
•Human atlas of limb skeletal muscle in embryonic, fetal, and adult tissues
•Human limb skeletal muscle populations and supportive cells vary across development
•PAX7 muscle progenitor and stem cells are not identical across developmental states
•hPSC-PAX7 cells align to the embryonic-to-fetal transition in human development
The study, published in the peer-reviewed journal Cell Stem Cell, identified various cell types present in skeletal muscle tissues, from early embryonic development all the way to adulthood. Focusing on muscle progenitor cells, which contribute to muscle formation before birth, and muscle stem cells, which contribute to muscle formation after birth and to regeneration from injury throughout life, the group mapped out how the cells’ gene networks — which genes are active and inactive — change as the cells mature.
The roadmap is critical for researchers who aim to develop muscle stem cells in the lab that can be used in regenerative cell therapies for devastating muscle diseases, including muscular dystrophies, and sarcopenia, the age-related loss of muscle mass and strength.
“Muscle loss due to aging or disease is often the result of dysfunctional muscle stem cells,” said April Pyle, senior author of the paper and a member of the Broad Stem Cell Research Center. “This map identifies the precise gene networks present in muscle progenitor and stem cells across development, which is essential to developing methods to generate these cells in a dish to treat muscle disorders.”
Researchers in Pyle’s lab and others around the world already have the capacity to generate skeletal muscle cells from human pluripotent stem cells — cells that have the ability to self-renew and to develop into any cell type in the body. However, until now, they had no way of determining where these cells fall on the continuum of human development.
“We knew that the muscle cells we were making in the lab were not as functional as the fully matured muscle stem cells found in humans,” said Haibin Xi, first author of the new paper and an assistant project scientist in Pyle’s lab. “So we set out to generate this map as a reference that our lab and others can use to compare the genetic signatures of the cells we are creating to those of real human skeletal muscle tissue.”
To create this resource, the group gathered highly specific data about two different groups of skeletal muscle cells: those from the human body, ranging from the fifth week of embryonic development to middle age, and those derived from human pluripotent stem cells the researchers generated in the lab. They then compared the genetic signatures of cells from both sources.
The group obtained 21 samples of human skeletal muscle tissue from their UCLA collaborators and from colleagues at the University of Southern California and the University of Tübingen in Germany. For the pluripotent stem cell-derived muscle cells, the group evaluated cells created using their own unique method and the methods of several other groups.
The Pyle lab collaborated with the lab of Kathrin Plath, a UCLA professor of biological chemistry and member of the Broad Stem Cell Research Center, to conduct high-throughput droplet-based single-cell RNA sequencing of all of the samples. This technology enables researchers to identify the gene networks present in a single cell and can process thousands of cells at the same time. Leveraging the power of this technology and the Plath lab’s bioinformatics expertise, the group identified the genetic signatures of various cell types from human tissues and pluripotent stem cells.
They next developed computational methods to focus on muscle progenitor and stem cells and mapped out their gene networks associated with every developmental stage. This enabled the group to match the genetic signatures found in the pluripotent stem cell-derived muscle cells with their corresponding locations on the map of human muscle development.
The group found that pluripotent stem cell-derived muscle cells produced by all the methods they tried resembled muscle progenitor cells at an early developmental state and did not align to adult muscle stem cells.
In addition to pinning down the true maturity of the lab-produced cells, this analysis also provided details about the other cell types present in skeletal muscle tissue across development and in populations derived from human pluripotent stem cells. These cells could play an essential role in muscle cell maturation and could be critical to improving methods to generate and support muscle stem cells in a dish.
“We found that some methods to generate muscle cells in a dish also produce unique cell types that likely support the muscle cells,” said Pyle, who is also a member of the UCLA Jonsson Comprehensive Cancer Center. “And so now our questions are, what are these cells doing? Could they be the key to producing and supporting mature and functional muscle stem cells in a dish?”
Adult chondrogenesis and spontaneous cartilage repair in the skate, Leucoraja erinacea
by Aleksandra Marconi, Amy Hancock-Ronemus, J Andrew Gillis Is a corresponding author, Department of Zoology, University of Cambridge, United Kingdom; Charles River Laboratories, United States; Marine Biological Laboratory, United States
Unlike humans and other mammals, the skeletons of sharks, skates, and rays are made entirely of cartilage and they continue to grow that cartilage throughout adulthood. New research finds that adult skates go one step further than cartilage growth: They can also spontaneously repair injured cartilage. This is the first known example of adult cartilage repair in a research organism. The team also found that newly healed skate cartilage did not form scar tissue.
And new research finds that adult skates go one step further than cartilage growth: They can also spontaneously repair injured cartilage. This is the first known example of adult cartilage repair in a research organism. The team also found that newly healed skate cartilage did not form scar tissue.
“Skates and humans use a lot of the same genes to make cartilage. Conceivably, if skates are able to make cartilage as adults, we should be able to also,” says Andrew Gillis, senior author on the study and a Marine Biological Laboratory Whitman Center Scientist from the University of Cambridge, U.K.
The researchers carried out a series of experiments on little skates (Leucoraja erinacea) and found that adult skates have a specialized type of progenitor cell to create new cartilage. They were able to label these cells, trace their descendants, and show that they give rise to new cartilage in an adult skeleton.
Why is this important? There are few therapies for repairing cartilage in humans and those that exist have severe limitations. As humans develop, almost all of our cartilage eventually turns into bone. The stem cell therapies used in cartilage repair face the same issue — the cells often continue to differentiate until they become bone. They do not stop as cartilage. But in skates, the stem cells do not create cartilage as a steppingstone; it is the end result.
“We’re looking at the genetics of how they make cartilage, not as an intermediate point on the way to bone, but as a final product,” says Gillis.
The research is in its early stages, but Gillis and his team hope that by understanding what genes are active in adult skates during cartilage repair, they could better understand how to stop human stem-cell therapies from differentiating to bone.
The EU not ready for the release of Gene drive organisms into the environment
Within the last decades, new genetic engineering tools for manipulating genetic material in plants, animals and microorganisms are getting large attention from the international community, bringing new challenges and possibilities. While genetically modified organisms (GMO) have been known and used for quite a while now, gene drive organisms (GDO) are yet at the consideration and evaluation stage.
The difference between these two technologies, where both are meant to replace certain characters in animals or plants with ones that are more favourable for the human population, is that, even though in GDO there is also foreign “synthetic” DNA being introduced, the inheritance mode differs. In GDO, the genome’s original base arrangements are changed, using CRISPR/Cas-9 genome editing. Once the genome is changed, its alterations are carried down the organism’s offspring and subsequent generations.
In their study, published in the open-access journal BioRisk, an international group of scientists led by Marion Dolezel from the Environment Agency Austria, discuss the potential risks and impacts on the environment.
The research team also points to current regulations addressing invasive alien species and biocontrol agents, and finds that the GMO regulations are, in principle, also a useful starting point for GDO.
There are three main areas suggested to benefit from gene drive systems: public health (e.g. vector control of human pathogens), agriculture (e.g. weed and pest control), environmental protection and nature conservation (e.g. control of harmful non-native species).
In recent years, a range of studies have shown the feasibility of synthetic CRISPR-based gene drives in different organisms, such as yeast, the common fruit fly, mosquitoes and partly in mammals.
Given the results of previous research, the gene drive approach can even be used as prevention for some zoonotic diseases and, hence, possible future pandemics. For example, laboratory tests showed that the release of genetically modified mosquitoes can drastically reduce the number of malaria vectors. Nevertheless, potential environment and health implications, related to the release of GDO, remain unclear. Only a few potential applications have so far progressed to the research and development stage.
“The potential of GDOs for unlimited spread throughout wild populations, once released, and the apparently inexhaustible possibilities of multiple and rapid modifications of the genome in a vast variety of organisms, including higher organisms such as vertebrates, pose specific challenges for the application of adequate risk assessment methodologies,” shares the lead researcher Mrs. Dolezel.
In the sense of genetic engineering being a fastly developing science, every novel feature must be taken into account, while preparing evaluations and guidance, and each of them provides extra challenges.
Today, the scientists present three key differences of gene drives compared to the classical GMO:
1. Introducing novel modifications to wild populations instead of “familiar” crop species, which is a major difference between “classic” GMOs and GDOs.
“The goal of gene drive applications is to introduce a permanent change in the ecosystem, either by introducing a phenotypic change or by drastically reducing or eradicating a local population or a species. This is a fundamental difference to GM crops for which each single generation of hybrid seed is genetically modified, released and removed from the environment after a relatively short period,” shares Dolezel.
2. Intentional and potentially unlimited spread of synthetic genes in wild populations and natural ecosystems.
Gene flow of synthetic genes to wild organisms can have adverse ecological impact on the genetic diversity of the targeted population. It could change the weediness or invasiveness of certain plants, but also threaten with extinction the species in the wild.
Possibility for long-term risks to populations and ecosystems.
Key and unique features of GDOs are the potential long-term changes in populations and large-scale spread across generations.
In summary, the research team points out that, most of all, gene drive organisms must be handled extremely carefully, and that the environmental risks related to their release must be assessed under rigorous scrutiny. The standard requirements before the release of GDOs need to also include close post-release monitoring and risk management measures.
It is still hard to assess with certainty the potential risks and impact of gene drive applications on the environment, human and animal health. That’s why highly important questions need to be addressed, and the key one is whether genetically driven organisms are to be deliberately released into the environment in the European Union. The High Level Group of the European Commission’s Scientific Advice Mechanism highlights that within the current regulatory frameworks those risks may not be covered.
The research group recommends the institutions to evaluate whether the regulatory oversight of GMOs in the EU is accomodate to cover the novel risks and challenges posed by gene drive applications.
Autism Linked to Group of Dysregulated Synapse and Neurotransmitter Release Genes
Researchers in Brazil have identified a group of co-expressed genes that are dysregulated in induced pluripotent stem cell (iPSC)-derived neuronal cells from patients with autism spectrum disorder (ASD), and which could potentially be used as a biomarker or even therapeutic target for the neurodevelopmental disorder. The study results, reported by scientists at the University of São Paulo’s Institute of Biosciences (IB-USP), indicate that a common gene expression profile my underpin ASD, regardless of the DNA mutations in any autistic individual.
The results indicate that while the DNA of individuals with autism may harbor different alterations, the activity of these genes is similar in people with the disorder, and differs from that of the same genes in the brains of people without autism. The investigators reported on their study in Molecular Psychiatry, in a paper titled, “Transcriptome of iPSC-derived neuronal cells reveals a module of co-expressed genes consistently associated with autism spectrum disorder.”
“We found a group of genes that’s dysregulated in neural progenitor cells, which give rise to neurons, and in neurons themselves,” said Maria Rita dos Santos e Passos-Bueno, PhD, a professor at IB-USP. “The study bore out the hypothesis that, while the origin of autism is multifactorial and different in each person, these different alterations can lead to the same problems in the functioning of their neurons,” added first author Karina Griesi Oliveira, PhD, a researcher in the Albert Einstein Israeli Education and Research Institute (IIEP).
ASD is a neurodevelopmental disorder that affects at least 1% of the population, and is characterized by impaired social-communicative skills and by repetitive behaviors, the authors wrote. Diagnosis of suspected cases generally can’t be made through imaging or blood tests, and while it has long been recognized that genetic factors play an important role in ASD, considerable variability in genetic background makes diagnosis and treatment of the disorder on a genomic basis difficult. About 100 genes have already been linked with the disorder, and another thousand are being studied, the investigators noted. “A major genetic error causes autism in some 30% of patients, but the origin of the disorder is multifactorial in 70%, with several alterations to DNA causing clinical symptoms, so that interpretation of the genetic data is still complex,” Passos-Bueno explained.
Despite the large number of candidate ASD-associated genes, there does seem to be some convergence on a few final common effectors or molecular pathways, however, “… suggesting that the different genetic variants associated with the disease may lead to similar functional consequences which might be reflected in the transcriptional level, protein level or, lately, in the regulation of specific cellular mechanisms,” the team commented.
Whole transcriptome studies carried out to investigate differentially expressed gene profiles associated with ASD have mainly used post-mortem brain tissue from ASD individuals, but this doesn’t capture ASD-related dysregulated gene expression that may occur only transiently during prenatal development. More recent developments in cellular reprogramming mean that it is now possible to generate neural progenitor cells (NPCs) and neurons from ASD patients, as in vitro models that might better recapitulate the features of the developing brain.
For their study, the team generated iPSC lineages from stem cells derived from teeth. “We took dental pulp cells from people with and without autism, and from these, we created pluripotent stem cells, which can be transformed into any type of cell,” said Oliveira. “In this way, we were able to create in the laboratory neural cells with the same genomes as those of the patients.”
Five individuals with high-functioning autism and one with low-functioning autism were enrolled in the study. The six individuals had heterogeneous genetic profiles. A control group comprised of six healthy subjects. The iPSCs derived from the tooth stem cells were reprogrammed into cell types that would simulate two stages in the development of the human brain, i.e., neural progenitor cells, which give rise to neurons, and neurons at a stage equivalent to those of a fetus between the 16th and 20th weeks of gestation.
The researchers then analyzed the transcriptomes of the neural progenitor cells and neurons. “By counting the RNA molecules, we were able to determine gene expression with a considerable degree of precision,” Oliveira said. Using mathematical models to determine which genes were differentially expressed between the groups with and without autism, the researchers highlighted genes involved in synaptic function and neurotransmitter release, essentially, a group of genes that modulates communication among neurons, which influences brain function. “Taken together, these exploratory analyses point to some putative proteins that may act as molecular links between NPC and neuron transcriptome dysregulation seen in ASD patients,” the investigators commented.
The set of genes identified, some of which have been linked with autism in previous research, displayed increased activity in neurons. “Some of them were dysregulated in iPSC-derived neural cells from autists studied in other research, and in neurons from postmortem brain tissue belonging to individuals with autism, validating the method,” Passos-Bueno said. “Although these results should be interpreted with caution due to the limited number of samples included in this analysis, these possible molecular regulatory links between modules in NPC and in neurons deserve further investigation,” the authors stated.
Interestingly, a second analysis using postmortem tissue data showed decreased gene expression at the time of death. “We don’t know the reason for the difference, but it’s consistent evidence that expression of this group of genes is involved in autism spectrum disorder,” Oliveira commented. “Comparison of our results with previous transcriptome studies using both iPSC-derived neuronal cells and postmortem brain tissue revealed the consistent dysregulation of a module of synaptic molecules, which may represent a subset of genes exhibiting a pattern of expression that could be used as a biomarker for ASD,” the team concluded.
The dysregulation appeared to affect communication among neurons in the subjects of the study, which was conducted in Brazil. The discovery could improve diagnosis, which is currently based on the clinical analysis of symptoms. [RIDC HUG-CELL]
The results provided additional evidence to suggest that autism begins to develop during gestation. “The study points to a disturbance in fetal neurodevelopment that alters neuronal functioning, so that the child is born with altered gene expression,” suggested Passos-Bueno, who is affiliated with the Human Genome and Stem Cell Research Center (HUG-CELL), a Research, Innovation and Dissemination Center (RIDC) supported by São Paulo Research Foundation — FAPESP and hosted by the University of São Paulo (USP).
New Retinal Imaging System May Be Used to Detect an Alzheimer’s Biomarker
Biomedical engineers at Duke University say they have devised a new imaging device capable of measuring both the thickness and texture of the various layers of the retina at the back of the eye. The advance could be used to detect a biomarker of Alzheimer’s disease, potentially offering a widespread early warning system for the disease, according to the team which published its study, “Multimodal Coherent Imaging of Retinal Biomarkers of Alzheimer’s Disease in a Mouse Model,” in Scientific Reports.
“We acquired depth-resolved light scattering measurements from the retinas of triple transgenic Alzheimer’s Disease (3xTg-AD) mice and wild type (WT) age-matched controls using co-registered angle-resolved low-coherence interferometry (a/LCI) and optical coherence tomography (OCT). Angle-resolved light scattering measurements were acquired from the nerve fiber layer, outer plexiform layer, and retinal pigmented epithelium using image guidance and segmented thicknesses provided by co-registered OCT B-scans. Analysis of the OCT images showed a statistically significant thinning of the nerve fiber layer in AD mouse retinas compared to WT controls. The a/LCI scattering measurements provided complementary information that distinguishes AD mice by quantitatively characterizing tissue heterogeneity,” the investigators wrote.
“The AD mouse retinas demonstrated higher mean and variance in nerve fiber layer light scattering intensity compared to WT controls. Furthermore, the difference in tissue heterogeneity was observed through short-range spatial correlations that showed greater slopes at all layers of interest for AD mouse retinas compared to WT controls. A greater slope indicates a faster loss of spatial correlation, suggesting a loss of tissue self-similarity characteristic of heterogeneity consistent with AD pathology. Use of this combined modality introduces unique tissue texture characterization to complement development of future AD biomarker analysis.”
“Previous research has seen a thinning of the retina in Alzheimer’s patients, but by adding a light-scattering technique to the measurement, we’ve found that the retinal nerve fiber layer is also rougher and more disordered,” said Adam Wax, PhD, professor of biomedical engineering at Duke. “Our hope is that we can use this insight to create an easy and cheap screening device that wouldn’t only be available at your doctor’s office, but at places like your local pharmacy as well.”
Diagnoses of Alzheimer’s disease are currently only made after a patient begins to show symptoms of cognitive decline. Even then, the only way to definitively determine that Alzheimer’s was the cause is with expensive MRI and PET scans or through an autopsy. But if disease progress can be halted through early interventions such as drugs and mental exercise, patients can have a greatly improved quality of life. This is why researchers are looking for biomarkers that could be used as early warning signs of the disease.
One such potential biomarker comes from the retina, which is literally an extension of the brain and part of the central nervous system. Previous research has shown that Alzheimer’s can cause structural changes to the retina, most notably a thinning of the inner retinal layers.
“The retina can provide easy access to the brain, and its thinning can be indicative of a decrease in the amount of neural tissue, which can mean that Alzheimer’s is present,” said Wax.
Other diseases such as glaucoma and Parkinson’s disease, however, can also cause a thinning of the retina. Inconsistent test results might also come from differences between the machines most often used for these types of measurements, optical coherence tomography (OCT) devices, and how researchers use them.
In the new paper, Wax and his graduate student Ge Song showed that the topmost layer of neurons in the retina of a mouse model of Alzheimer’s disease exhibit a change in their structural texture. Combined with data on the changes in thickness of this layer, the new measurement could prove to be a more easily accessible biomarker of Alzheimer’s.
“Our new approach can measure the roughness or texture of the nerve fiber layer of the inner retina,” noted Song. “It can provide a quick and direct way to measure structural changes caused by Alzheimer’s, which has great potential as a biomarker of the disease.”
OCT is the optical analog of ultrasound. It works by sending waves of light into tissues and measuring how long they take to come back. While it is an extremely useful imaging technique commonly used to make a wide array of diagnoses, it has limitations.
To gather more data, Wax and Song added a measurement called angle-resolved low-coherence interferometry (a/LCI), which uses the angles of the scattered light to gather more information about the tissue’s structure. By combining the two measurements, the researchers can extract both thickness and structural information about each layer of the retina.
“The a/LCI measurements complement the thickness measurements to improve the potential utility of more quantitative biomarkers for Alzheimer’s,” according to Song. “You can’t get textural and structural information about the retina with OCT alone. You need both imaging modalities. That’s the key innovation.”
Good News for COVID-19 Vaccine: Immune System Shows Robust Response to SARS-CoV-2:
Information about immunity to SARS-CoV-2, both in the context of COVID-19 disease pathogenesis and in the context of how to develop a good vaccine, remains limited. But developing a vaccine and predicting how the coronavirus pandemic will unfold until such a vaccine is available are both contingent upon the understanding of whether the immune system can mount a substantial and lasting response to SARS-CoV-2 and whether exposure to other, common, circulating coronaviruses provides any kind of protective immunity.
A collaboration between the labs of Alessandro Sette, Dr. Biol. Sci., professor in the Center for Infectious Disease and Vaccine Research, and Shane Crotty, PhD, professor at La Jolla Institute for Immunology, is starting to fill in the massive knowledge gap and is providing the first cellular immunology data.
Their work, published in Cell in a paper titled, “Targets of T cell responses to SARS-CoV-2 coronavirus in humans with COVID-19 disease and unexposed individuals,” studied T cell and antibody immune responses in average COVID-19 cases.
The study documents a robust antiviral immune response to SARS-CoV-2 in a group of 20 adults who had recovered from COVID-19. The findings show that the body’s immune system is able to recognize SARS-CoV-2 in many ways, dispelling fears that the virus may elude ongoing efforts to create an effective vaccine.
The findings are “good news”, tweeted Crotty, for “coronavirus vaccine development, understanding disease, and even modeling the future course of the pandemic.”
They also showed that 100% of COVID-19 cases made antibodies and CD4 T cells. Also, 70% of COVID-19 cases made measurable CD8 T cells. “Our data show that the virus induces what you would expect from a typical, successful antiviral response,” said Crotty.
They also found CD4+ T-cell responses to spike, the main target of most vaccine efforts, were robust, and correlated with the magnitude of the anti-SARS-CoV-2 IgG and IgA titers.
“If we had seen only marginal immune responses, we would have been concerned,” said Sette, and added, “but what we see is a very robust T-cell response against the spike protein, which is the target of most ongoing COVID-19 efforts, as well as other viral proteins.”
“All efforts to predict the best vaccine candidates and fine-tune pandemic control measures hinge on understanding the immune response to the virus,” said Crotty, also a professor in the Center for Infectious Disease and Vaccine Research. “People were really worried that COVID-19 doesn’t induce immunity, and reports about people getting re-infected reinforced these concerns, but knowing now that the average person makes a solid immune response should largely put those concerns to rest.”
In an earlier study, Sette and his team had used bioinformatics tools to predict which fragments of SARS-CoV-2 are capable of activating human T cells. The scientists then, in this latest research, tested whether T cells isolated from adults who had recovered from COVID-19 without major problems, recognized the predicted protein fragments, or so-called peptides, from the virus itself. The scientists pooled the peptides into two big groups: The first so-called mega-pool included peptides covering all proteins in the viral genome apart from SARS-CoV-2’s “spike” protein. The second mega-pool specifically focused on the spike protein that dots the surface of the virus, since almost all of the vaccines under development right now target this coronavirus spike protein.
“We specifically chose to study people who had a normal disease course and didn’t require hospitalization to provide a solid benchmark for what a normal immune response looks like, since the virus can do some very unusual things in some people,” said Sette.
The teams also looked at the T-cell response in blood samples that had been collected between 2015 and 2018, before SARS-CoV-2 started circulating. They detected SARS-CoV-2-reactive CD4+ T cells in ~50% of unexposed individuals. But everybody has almost certainly seen at least three of the four common cold coronaviruses, which could explain the observed crossreactivity.
Any potential for crossreactive immunity from other coronaviruses has been predicted by epidemiologists to have significant implications for the pandemic going forward. Crossreactive T cells are also relevant for vaccine development, as cross-reactive immunity could influence responsiveness to candidate vaccines.
Whether this immunity is relevant in influencing clinical outcomes is unknown, tweeted Crotty, but it is tempting to speculate that the crossreactive CD4+ T cells may be of value in protective immunity, based on SARS and flu data.
Improving the Pneumococcus Vaccine:
Vaccines that protect people from infection by Streptococcus pneumoniae, which kills up to one million children ever year worldwide, train the immune system to recognize the pathogen’s thick sugar capsule. Pneumococcus capsules are not only the active ingredient in vaccines; they’re also key to the pathogen’s virulence.
But different strains have different capsules, which means vaccine researchers need to identify all capsule types. Pneumococcus experts at the University of Alabama at Birmingham describe “A New Pneumococcal Capsule Type, 10D, is the 100th Serotype and Has a Large cps Fragment from an Oral Streptococcus” in mBio, a newly-found capsule — the 100th to be identified since the pathogen was first discovered in the late 19th century.
“Streptococcus pneumoniae (pneumococcus) is a major human pathogen producing structurally diverse capsular polysaccharides. Widespread use of highly successful pneumococcal conjugate vaccines (PCVs) targeting pneumococcal capsules has greatly reduced infections by the vaccine types but increased infections by nonvaccine serotypes,” write the investigators.
“Herein, we report a new and the 100th capsule type, named serotype 10D, by determining its unique chemical structure and biosynthetic roles of all capsule synthesis locus (cps) genes. The name 10D reflects its serologic cross-reaction with serotype 10A and appearance of cross-opsonic antibodies in response to immunization with 10A polysaccharide in a 23-valent pneumococcal vaccine.
“Genetic analysis showed that 10D cps has three large regions syntenic to and highly homologous with cps loci from serotype 6C, serotype 39, and an oral streptococcus strain (S. mitis SK145). The 10D cps region syntenic to SK145 is about 6 kb and has a short gene fragment of wciNα at the 5′ end. The presence of this nonfunctional wciNα fragment provides compelling evidence for a recent interspecies genetic transfer from oral streptococcus to pneumococcus.”
“Since oral streptococci have a large repertoire of cps loci, widespread PCV usage could facilitate the appearance of novel serotypes through interspecies recombination.”
Moon Nahm, MD, who led the study, said identifying new capsules is critical to keep up with the rapidly changing bacteria and update vaccines that can save lives.
Current pneumococcal vaccines contain 10–13 different types of capsules, and they cause a person’s immune system to produce antibodies against those capsules. “If you get rid of the capsules, then the bugs cannot cause the infection,” Nahm said.
But pneumococcus is a moving and constantly evolving target. As vaccines vanquish some capsules, new ones emerge that can shield the virus from the immune system. As a result, the vaccines become less effective, and the pathogen still poses a serious threat, even to immunized children.
“Pneumococcus is smart,” explained Nahm. “It’s critical for scientists to know about different capsule types.” In the last decade or so, Nahm’s lab in Birmingham, which is recognized as a reference lab by the World Health Organization (WHO), has identified 10 new capsules. His research focuses on finding ways to make vaccines both more effective and less expensive. (The current pneumococcal vaccine costs about $100 per dose, putting it out of reach for many children in low-income countries.)
Nahm and his collaborators discovered the new capsule after being contacted by the Global Pneumococcal Sequencing (GPS) project. With funding from the Bill and Melinda Gates Foundation, GPS researchers had sequenced the genomes of more than 20,000 pneumococci strains. When those researchers found strains with capsule genes they didn’t recognize, they sent the strains to Nahm’s group, which identified the new and 100th capsule structure.
Do Malaria Parasites Have an Inherent Sense of Time?
Most organisms have a biological rhythm — and not the kind your uncle thinks he has when he starts dancing at weddings and family gatherings. These rhythms often control metabolic events at the cellular level and can be particularly important for parasites to complete their intricate lifecycles. No parasites, and few other organisms, are as deadly as malaria, so understanding its molecular clock could open up new treatment approaches.
Now, a team of investigators led by scientists at UT Southwestern has uncovered that the malaria parasite is driven by its own inherent clock. This discovery overturns decades of conventional wisdom about malaria, as the prevailing theory has been that the parasite takes its cues from its animal hosts. Findings from the new study were published recently in Science through an article titled, “The malaria parasite has an intrinsic clock.”
It’s long been known that malaria induces cyclical fevers, which occur every two to three days in human hosts, depending on the species of infecting organism. This is the result of all the parasites simultaneously bursting the red blood cells of the host they infect.
“It’s as if the entire parasite is under this 24-hour program,” noted senior study investigator Joseph Takahashi, PhD, professor and chair of neuroscience at UT Southwestern. “We think that if we can figure out what controls that program, we’d have a new target to try to inhibit the life cycle of the parasite.”
Circadian clocks, which control metabolism on a daily rhythm, are important in virtually all living things, from bacteria to plants and animals. But little is known about the role of daily rhythms in parasites, which also have to contend with their hosts’ clocks.
In malaria, Plasmodium parasites grow inside the host’s red blood cells and destroy them, triggering fevers and other symptoms. Doctors have long noticed that these fevers are rhythmic, recurring every 24, 48, or 72 hours depending on the species of Plasmodium. But scientists have assumed the parasite merely follows its host’s 24-hour rhythm.
Takahashi, who discovered the genetic basis for mammals’ circadian clocks in the 1990s, suspected that the parasite might set its own rhythm. He and postdoc Filipa Rijo-Ferreira had observed something similar in another kind of parasite.
Rijo-Ferreira and Takahashi discovered in 2017 that the parasite that causes sleeping sickness has its own circadian rhythm. In 2018, they reported that the parasite shifts its host’s circadian clock, making people sleep during the day instead of at night. The idea that parasites have internal clocks “just exploded my imagination,” Rijo-Ferreira stated. Until then, no one had reported such a timing mechanism in a parasite. After that, malaria, with its cycling fevers, seemed like the most promising place to look.
“We showed that parasite rhythms are flexible and lengthen to match the rhythms of hosts with long circadian periods,” the authors wrote. “We also show that malaria rhythms persist even when host food intake is evenly spread across 24 hours, suggesting that host feeding cues are not required for synchrony. Moreover, we find that the parasite population remains synchronous and rhythmic even in an arrhythmic clock mutant host. Thus, we propose that parasite rhythms are generated by the parasite, possibly to anticipate its circadian environment.”
The researchers conducted a series of experiments using mice and the malaria parasite that infects them, Plasmodium chabaudi. First, they demonstrated that the parasite’s rhythm persists in constant darkness and regardless of host feeding, with 4,000 of the parasite’s roughly 5,000 genes cycling in their levels of activity. Then they showed that the parasite can shift its daily rhythm and that its rhythm persists even in mice genetically altered to have no rhythm of their own.
The researchers saw that of the 5,244 genes expressed by the blood stage of Plasmodium, more than 80% had the same cyclic patterns of expression in both lighting conditions. The activity of these genes peaked at the same time and with the same intensity in both groups, suggesting that the lighting cues that drive biological clocks in their mouse hosts weren’t affecting rhythms for the parasites.
To see if the clock in Plasmodium still ran about 24 hours, even if the clocks in their hosts do not, the researchers studied the parasite’s gene activity in mice with a genetic mutation that causes their own circadian rhythms to run about 26 hours instead of the usual 24. Tests showed that the protozoa seemed to slow their cell cycles to match those of their hosts, stretching them out to cover the 26-hour period. However, this correlation wasn’t perfect — Plasmodium‘s gene expression lagged behind, taking several days to catch up with its long-period host. These findings suggest that although the parasite seems to take cues from its host, it still ran on its own time.
MISC
Introducing New Bioprocessing Technologies in the Era of COVID-19:
Bioprocessing is undergoing dramatic changes as companies develop new manufacturing strategies; according to Artur Miguel Arsenio, PhD, head of product management at Sartorius Stedim Biotech. “The digitalization of several elements of our value chain is transforming the way we operate and meet our customers’ needs,” he told GEN. “With the end-to-end integration of systems and data, we are introducing bundling and cross-selling of multiple systems, including digital companions.”
A critical feature of the Bioprocessing 4.0 concept is the reduction of human error. “The increase of automation, remote diagnostics, real-time process monitoring and control can significantly reduce the need for manual tasks,” he stated, “thus decreasing the risks for an important source of contamination. Furthermore, automation and smart connected systems empower the performance of human workers on manual tasks, helping them to avoid errors and reducing risks.”
The company predicts that flexible automation integration will reduce the project effort for installing an upstream /downstream bioprocessing facility by 50–75% because activities are substantially reduced during the integration. The modular packages allow rapid and flexible deployment or change of various consumable configurations to allow process adaptation and quick system upgrades.
“Tailored configurations can be easily updated with a simple software change, even in a cGMP environment,” Arsenio continued. “These smart modular package units allow us to override manual set-up and running issues, significantly reducing human error during set-up and process runs.”
A better process understanding also helps to limit the number of actions dependent on humans (and options offered), further reducing opportunities for errors. Data analytics tools enable process optimization, further reducing the need for human intervention, and the quality by design strategy reduces the risk of failed batches due to increased process understanding and therefore reduces costs.
For Arsenio, Bioprocessing 4.0 is a new concept, focusing on system and data connectivity in the biotech industries. “We believe it to be an enabler of transformative innovation within the industry (the way we work, our processes, our products and platforms). It brings the potential to react flexibly and in a scalable way to changing market demands and it aligns with the industry’s drive to significantly reduce CAPEX and OPEX associated with the manufacturing of lifesaving biopharmaceuticals to an expanding global market.”
Today the overriding challenge to the bioprocessing industry is the Coronavirus COVID-19 threat and the need to ramp of production rapidly.
“Sartorius’ Ambr systems are helping the industry to speed up process development to reach clinical trials. PAT (Process Analytical Technology) also plays an important role,” maintains Arsenio. “Furthermore, the market demands of the COVID-19 pandemic call for significant improvements, such as time-to-clinic and time-to-facility. A proper layout of automation can improve time-to-facility, by bringing options for faster integration. Biobrain, a new automation platform for our biomanufacturing systems, is a smart modular package unit, engineered to ensure seamless integration of SU instruments into different supervisory control and data acquisition (SCADA) or Digital Control System (DCS).”
COVID-19 Drives CRISPR Diagnostics:
Mammoth Biosciences is responding to the urgent need for improved and more accessible testing for COVID-19 by rapidly reconfiguring the company’s CRISPR-based diagnostics platform to detect the presence of SARS-CoV-2. In April, the company published a study demonstrating the power of its DNA endonuclease-targeted CRISPR trans reporter (DETECTR) system to detect SARS-CoV-2 from respiratory swab RNA extracts in under 45 minutes in the largest set of patient samples to date. The article’s authors asserted that DETECTR provides a visual and faster alternative to the CDC’s SARS-CoV-2 real-time RT-PCR assay, with 95% positive predictive agreement and 100% negative predictive agreement.
Smart AI Use Could Benefit Biopharma:
The biopharmaceutical industry is no stranger to artificial intelligence (AI) and machine learning, particularly in the discovery lab. But AI could also improve manufacturing, said Julia Rozenbaum, business development researcher and data analyst at Sigmoidal, a consulting group.
“AI has the potential to impact each step of the drug production process. It might be the most crucial to the first stages,” she explained. “Algorithms can predict interactions between molecules to understand mechanisms of disease. This can help to find new drug components. AI might also be of use in running preclinical tests. That could shorten the time to develop and launch new medicines.”
AI also has the potential to streamline processes on the biomanufacturing facility factory floor and distribution center, said Rozenbaum, noting that “When it comes to the manufacturing process itself, AI can process in real-time the vast amount of data that is being produced. It can lead to improved supply chain planning, forecasting, inventory management, and basically help to speed up and automate every step of the process.”
Barry Heavy, a managing director in Accenture’s life sciences practice, also sees a role for AI in manufacturing.
“In the future, AI could help deconvolute the complex biology in the bioreactor — helping to understand the correlation between the culture conditions, the physiology of the producer cells, and the yield and quality attributes of the final product,” he told GEN. “AI will also help manufacturers gain a better understanding of causal relationships, which in turn may help develop more consistent, higher yield processes more quickly in process development and speed up root cause determination when there are issues with existing processes in routine commercial manufacturing.”
But the biopharmaceutical industry is yet to embrace AI. In fact, the approach is not even close to being commonplace, according to Heavy, who said the industry is struggling to find the best way to record, manage, and interpret the vast amount of data generated during the manufacturing process.
“We are still in early days when it comes to using AI in biotech manufacturing. Indeed, some companies are still trying to roll out standard multivariate analysis” he added.
According to Daniel Faggella, founder of Emerj Artificial Intelligence Research, biopharma struggles to implement AI on the factory floor.
“As far as I know, no company has integrated AI so thoroughly as to have either massively improved, or massively screwed up their operations. Of course, that information would be hard to find either way,” he pointed out. “There are a lot of initiatives and investments, but little by way of concrete steps. One of the major challenges is determining how to integrate AI into workflows. Which phases of the process can we use AI to help improve human decisions? It’s all nascent so it’s hard to pick. It’s opportunity but also risk.”
Another difficulty is the lack of overlap between biopharma and computer science, Faggella said.
“Computer science and life science don’t communicate well,” he continued. There has not been enough ‘osmosis’ to allow these two groups to feel part of the same team. They are a foreign language, fighting for another team. Integrating cross-functional teams to work on pharma data science problems is critical.”
Smaller, innovative companies will lead the way in AI, predicts Faggella.
“I’m of the belief that we may need to build the pharma firm of the future from the ground up, like Benevolent.AI is trying to do — because the AI deployment in these behemoth firms is so slow and painstaking.”
AGC Biologics Partners with Faron Pharmaceuticals to Manufacture Cancer Treatment:
Faron Pharmaceuticals selected AGC Biologics, a CDMO, to commercially manufacture Clevegen, a humanized anti-Clever-1 antibody which targets CLEVER-1 positive tumor-associated macrophages (TAMs) and converts these immunosuppressive M2 macrophages to immune stimulating M1 macrophages. This macrophage-directed immuno-oncology switch may be used alone or in combination with other cancer treatments, according to a Faron official, who notes that data from Faron’s ongoing MATINS trial has shown that Clevegen is safe and well-tolerated, making it a low-risk candidate for combination with existing cancer therapies. Clevegen reportedly has also shown early clinical benefits in patients who have exhausted all other treatment options.
“We are pleased to initiate this collaboration with AGC Biologics aiming at industrial scale manufacturing of Clevegen,” says Markku Jalkanen, PhD, Faron’s CEO. “This allows flexible and cost-efficient manufacturing to fulfill the growing need in clinical development while ensuring rapid and regulatory-ready scale up of the production for commercial needs. At Faron, we feel it’s important to progress along the clinical development and report to the regulators (FDA, EMA) at the end of the phase II meeting for Clevegen. This could take place, depending on the MATINS study Part II results, as soon as H2–2020.”
“Our priority has always been to serve our customers with a strong commitment to continued innovation,” adds Patricio Massera, CEO of AGC Biologics. “We’re proud to be partnering with Faron on such an important treatment and sharing our decades of experience in commercial scale production of biotechnological products.”
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