John Sterling, Author at GEN - Genetic Engineering and Biotechnology News Leading the way in life science technologies Thu, 19 Oct 2023 16:20:50 +0000 en-US hourly 1 https://wordpress.org/?v=6.3 https://www.genengnews.com/wp-content/uploads/2018/10/cropped-GEN_App_Icon_1024x1024-1-150x150.png John Sterling, Author at GEN - Genetic Engineering and Biotechnology News 32 32 Genomes Reveal the Encounter between Neanderthals and Sapiens https://www.genengnews.com/topics/omics/genomes-reveal-the-encounter-between-neanderthals-and-sapiens/ Thu, 19 Oct 2023 16:20:38 +0000 https://www.genengnews.com/?p=275032 Modern humans (Homo sapiens) from Africa began replacing Neanderthals 40,000 years ago in the western part of the Eurasian continent where Neanderthals had lived for hundreds of thousands of years. The replacement was not sudden but took place over several millennia which resulted in the integration of Neanderthal DNA into the H. sapiens genome. Statistical analyses revealed subtle variations in time and geographical space.

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Scientists at the University of Geneva (UNIGE) have analyzed the distribution of the portion of DNA inherited from Neanderthals in the genomes of modern humans over the last 40,000 years. These statistical analyses revealed subtle variations in time and geographical space. This study, “Past human expansions shaped the spatial pattern of Neanderthal ancestry,” published in Science Advances, helps shed light on the common history of these two species.

Modern humans (Homo sapiens) from Africa began replacing Neanderthals 40,000 years ago in the western part of the Eurasian continent where Neanderthals had lived for hundreds of thousands of years. The replacement was not sudden but took place over several millennia which resulted in the integration of Neanderthal DNA into the H. sapiens genome.

“The worldwide expansion of modern humans started before the extinction of Neanderthals (Homo neanderthalensis). Both species coexisted and interbred, leading to slightly higher introgression in East Asians than in Europeans. This distinct ancestry level has been argued to result from selection, but range expansions of modern humans could provide an alternative explanation. This hypothesis would lead to spatial introgression gradients, increasing with distance from the expansion source,” write the researchers.

“We investigate the presence of Neanderthal introgression gradients after past human expansions by analyzing Eurasian paleogenomes. We show that the out-of-Africa expansion resulted in spatial gradients of Neanderthal ancestry that persisted through time. While keeping the same gradient orientation, the expansion of early Neolithic farmers contributed decisively to reducing the Neanderthal introgression in European populations compared to Asian populations. This is because Neolithic farmers carried less Neanderthal DNA than preceding Paleolithic hunter-gatherers. This study shows that inferences about past human population dynamics can be made from the spatiotemporal variation in archaic introgression.”

Genome sequencing and comparative analysis

Due to genome sequencing and comparative analysis, it’s established that Neanderthals and Sapiens interbred and that these encounters were sometimes fruitful, leading to the presence of about two percent of DNA of Neanderthal origin in present-day Eurasians. However, this percentage varies slightly between regions of Eurasia, since DNA from Neanderthals is somewhat more abundant in the genomes of Asian populations than in those of European populations.

One hypothesis to explain this difference is that natural selection would not have had the same effect on genes of Neanderthal origin in Asian and European populations. The team of Mathias Currat, PhD, senior lecturer in the department of genetics and evolution at the UNIGE Faculty of Science, is working on another hypothesis. His previous work, based on computer simulations, suggests that such differences could be explained by migratory flows: when a migrant population hybridizes with a local population, in their area of cohabitation, the proportion of DNA of the local population tends to increase with distance from the point of departure of the migrant population.

In the case of Sapiens and Neanderthals, the hypothesis is that the further one moves away from Africa, Homo sapiens’ point of origin, the greater the proportion of DNA from Neanderthal, a population mainly located in Europe. To test this hypothesis, the authors used a database made available by Harvard Medical School that includes more than 4,000 genomes from individuals who have lived in Eurasia over the past 40 millennia.

‘‘Our study is mainly focused on European populations since we are obviously dependent on the discovery of bones and the state of conservation of DNA. It turns out that archaeological excavations have been much more numerous in Europe, which greatly facilitates the study of the genomes of European populations,’’ explains Claudio Quilodrán, PhD, senior research and teaching assistant in the department of genetics and evolution at the UNIGE Faculty of Science, and co-first author of the study.

Paleolithic hunter-gatherers

Statistical analyses revealed that, in the period following the dispersal of Homo sapiens from Africa, the genomes of Paleolithic hunter-gatherers who lived in Europe contained a slightly higher proportion of DNA of Neanderthal origin than the genomes of those who lived in Asia. This result is contrary to the current situation but in agreement with paleontological data, since the presence of Neanderthals was mainly reported in western Eurasia (no Neanderthal bones have been discovered further east than the Altai region of Siberia).

Subsequently, during the transition to the Neolithic, i.e., the transition from the hunter-gatherer lifestyle to the farmer lifestyle, 10,000 to 5,000 years ago, the study shows a decline in the proportion of DNA of Neanderthal origin in the genomes of European populations, resulting in a slightly lower percentage than that of Asian populations (as currently observed). This decrease coincided with the arrival in Europe of the first farmers from Anatolia (Turkey’s western peninsula) and the Aegean area, who themselves carried a lower proportion of DNA of Neanderthal origin than the inhabitants of Europe at the same time. By mixing with the populations of Europe, the genomes of farmers from Anatolia “diluted’’ Neanderthal DNA a little more.

The study shows that the analysis of ancient genomes, coupled with archaeological data, makes it possible to trace different stages in the history of hybridized species. ‘‘In addition, we are beginning to have enough data to describe more and more precisely the percentage of DNA of Neanderthal origin in the genome of Sapiens at certain periods of prehistory. Our work can therefore serve as a reference for future studies to more easily detect genetic profiles that deviate from the average and might therefore disclose an advantageous or disadvantageous effect,’’ notes Currat, last author of the study.

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WuXi Biologics Launches New Bioprocessing Platform https://www.genengnews.com/topics/bioprocessing/wuxi-biologics-launches-new-bioprocessing-platform/ Thu, 19 Oct 2023 16:15:40 +0000 https://www.genengnews.com/?p=275005 The WuXiUI platform can be adopted and scaled up/out in existing facilities without additional requirements for major equipment or complex operations, bringing minimum changes to the downstream process, according to WuXi Biologics. WuXiUI applies an intermittent-perfusion fed-batch (UI-IPFB) strategy in upstream production that reportedly realizes a three- to six-fold increase in productivity in a typical culture duration of 14 days for a fed-batch process.

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Global CDMO WuXi Biologics launched a new proprietary bioprocessing platform WuXiUITM, which the company describes as “an ultra-intensified, fed-batch solution that enhances the productivity and quality of multiple different CHO or other mammalian cell lines and product modalities.”

WuXiUI applies an intermittent-perfusion fed-batch (UI-IPFB) strategy in upstream production to realize a three- to six-fold increase in productivity in a typical culture duration of 14 days for a fed-batch process for different molecule modalities such as monoclonals, bispecifics, and recombinant proteins, according to Chris Chen, PhD, company CEO. For example, by leveraging WuXiUI, the titer of a bispecific antibody achieved 25 g/L in 14 days (five times higher than the same-scale traditional fed-batch process), he added.

“WuXiUI reduces drug substance manufacturing COGS by an estimated 60–80 percent compared to traditional fed-batch processes in single-use bioreactors, enhancing the competitiveness of commercial products,” continues Chen. “The platform is also easily adopted and can be scaled up/out in existing facilities without additional requirements for major equipment or complex operations, bringing minimum changes to the downstream process. Adhering to WuXi Biologics’ ESG (environmental, social, governance) strategy, WuXiUI has a lower carbon footprint than traditional or other intensified fed-batch processes due to more efficient media consumption and reduced waste generation.”

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Forwarding Allogeneic Therapies https://www.genengnews.com/topics/bioprocessing/forwarding-allogeneic-therapies/ Wed, 18 Oct 2023 20:00:11 +0000 https://www.genengnews.com/?p=274951 Cytiva and Bayer share a vision of the challenges limiting the advancement of allogeneic cell therapy and believe that together they can overcome these challenges. The companies are collaborating to build a fully-automated, modular platform that can be utilized for scaleup and manufacturing of multiple cell therapy products. The concept will use fully-characterized individual equipment modules that can be incorporated in a plug-and-play scenario.

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By Mary Ann Labant

Producing living cells as a therapeutic product is a complex process. To date, autologous-based cells comprise the majority of clinically-evaluated CAR T-cell products. Although autologous therapies can indeed be effective and life-changing for patients, this approach poses time and logistics constraints. Allogeneic cell products, generated using cells from healthy donors, can potentially overcome these limitations and provide the generation of “off-the-shelf” products.

But the technologies, solutions, and equipment needed to bring allogeneic cell therapies to large-scale clinical trials and global commercialization are not yet commercially available and that is, besides the biological challenge to guarantee immune evasion of these cells, one of the key bottlenecks facing the industry.

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To capture the potential of using healthy donor stem cells as the basis for cell therapies, cells must be programmed in a way to avoid attack by the recipient’s immune system. [Stefania Pelfini, La Waziya Photography/Getty Images]
“Allogeneic stem cell therapy is exciting because a stem cell has the potential to differentiate into almost any kind of tissue cell and therefore can address the root cause of a huge variety of diseases,” said Thomas Bieringer, PhD, technical leader, Bayer.

To capture the potential of using healthy donor stem cells as the basis for cell therapies, cells must be programmed in a way to avoid attack by the recipient’s immune system. Recent developments in gene editing technologies support strategies to design immune evasion.

“So now, we have the basis for moving from a single-patient autologous therapy to a one-to-many allogeneic therapy. However, we need the technologies, solutions, and equipment to make that possible,” pointed out Aaron Dulgar-Tulloch, PhD, chief technology officer, Cytiva. Cytiva and Bayer share a vision and common view of the challenges limiting the advancement of allogeneic cell therapy and believe that together they can overcome these challenges.

The companies are collaborating to build a fully-automated, modular platform that can be utilized for scaleup and manufacturing of multiple cell therapy products. The concept will use fully-characterized individual equipment modules that can be incorporated in a plug-and-play scenario. Both Dulgar-Tulloch and Bieringer believe this will accelerate the learning curve.

Human cells are fragile

Dealing with living cells as a therapeutic product makes the processes more complex than traditional biotherapeutics. Depending on the therapeutic application, different types of cells must be processed. These cells, which may need to be grown as aggregates, cell suspensions, or single cells, show higher sheer and nutrient and waste sensitivity relative to classical bioproduction cell lines.

In essence, the cells want to “feel good” in the corresponding reactors, which means that they require the right media composition. In addition, oxygen transfer and metabolic stress need to be precisely controlled. To provide the cells the optimal environment both the underlying biological process and the equipment performance must be optimized.

biioreactor
By leveraging both companies’ strengths the joint process team brings together Bayer’s deep knowledge of the biology and the manufacturing requirements of living cells with Cytiva’s expertise in the development of robust and automated equipment solutions. [Dani Serrano/Getty Images]
The development of this user-focused manufacturing platform is intended to address the sensitivity and requirements of different cell systems, work with a variety of model systems comprising different cell types, and utilize a broad range of modeling and lab experimental tools.

 

Enabling genomic medicines

The collaboration is focused on what the companies envision the entire genomic medicine field needs to bring cell therapies to patients faster. “If we are successful, we believe the entire community of therapy developers, technology providers and most importantly, patients, will benefit from accelerated, cost-effective, and globally available, allogeneic cell therapies,” said Dulgar-Tulloch.

The process began by aligning on the boundary conditions of the platform, i.e., the way to define the modularity (hardware and software plug-and-play), the automation and the process control concept. The initial focus is on two components with a current immense need: a 3D expansion system for production at scale and a robust harvest solution. As additional needs are identified other devices may follow.

The ultimate goal is to gather insights and offer solutions to a wide range of users driving the creation of an allogeneic cell therapy consensus platform. Bieringer emphasized that this will drive economies of scale and simplify global manufacturing, ultimately driving down costs to make allogeneic cell therapies more accessible.

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In-Line Analytical Benefits and Challenges https://www.genengnews.com/topics/bioprocessing/in-line-analytical-benefits-and-challenges/ Wed, 18 Oct 2023 16:00:53 +0000 https://www.genengnews.com/?p=274795 In-line analysis provides benefits such as sample integrity, preserving costly media, reducing waste and contamination risk, and improving product quality. In addition, it saves operator time compared to labor-intensive manual sampling. However, scientists also need tools that provide timely measurements of critical process and product quality attributes. These include devices that offer easy-to-integrate in-line analysis and control without the need for substantial expert configuration.

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By Mike May, PhD

As bioprocessing moves forward, companies hope to keep better track of production. A key goal is in-line analysis. This “enables continuous monitoring and control of critical process parameters in upstream bioprocess development,” says Chris Brown, PhD, co-founder and chief product officer at 908 Devices. “In-line measurements of cell cultures occur directly in a bioreactor with no sample volume loss.”

As a result, in-line analysis provides many benefits. Brown mentions sample integrity, preserving costly media, reducing waste and contamination risk, and improving product quality. “In-line analysis also saves operator time compared to manual sampling, which is labor intensive,” Brown says.

In addition, in-line analysis allows bioprocessors to improve the control of production. As Brown notes, this form of analysis “provides real-time monitoring of a process, allowing for immediate corrective action to be taken along with rich data to better support efforts in predictive bioprocess modeling.”

Challenges remain

Nonetheless, challenges stand in the way of reaching that goal. “As the biopharmaceutical industry adopts process analytical technology—PAT—to drive the advancement of Biopharma 4.0, scientists need an array of tools that provide timely measurements of critical process and product quality attributes,” Brown says.

For now, scientists need better tools to accomplish these goals. “The power of Raman spectroscopy for in-line bioprocess analysis is well known, but the expense and expertise required to develop robust and sustainable multivariate models is a massive impediment,” Brown says. “For Biopharma 4.0 to advance, scientists need a suite of devices that offer easy-to-integrate in-line analysis and control without the need for substantial expert configuration.”

Fortunately, existing technology can address the challenges and realize the potential of in-line analysis.

Chris Brown, PhD, 908 Devices
Chris Brown, PhD, 908 Devices

“There are solutions available now that can offer all the advantages of Raman spectroscopy without the cost and complexities associated with conventional spectroscopic methods,” Brown says. “These are turn-key solutions that provide real-time, in-line monitoring and control of multiple bioprocess parameters with no modeling or development required.”

This approach relies on “purpose-built de novo models that automatically process Raman spectra from a wide variety of cell culture media types and cell lines, delivering actionable process parameters in minutes,” Brown says.

Overall, in-line analysis could transform much of bioprocessing. As Brown sums it up: “In-line analyzers enable biopharmaceutical process development scientists and manufacturers to enhance process understanding and implement dynamic control strategies quicker and easier.”

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Increasing Access to Cell Therapies https://www.genengnews.com/topics/bioprocessing/bedside-gmp-in-a-box-to-increase-cell-therapy-access/ Wed, 18 Oct 2023 16:00:34 +0000 https://www.genengnews.com/?p=274919 Good manufacturing practice in a box essentially condenses the complex cell therapy manufacturing process into a more compact and automated system that can be housed within a hospital. This not only automates an error-prone manual process but also eliminates the need to send cellular materials to centralized manufacturing facilities. This can reduce the cost associated with delivery of novel cell therapies like CAR-T to patients.

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By Gareth Macdonald

Making autologous cell therapies is a logistical challenge as much as a technical one. Material from the hospitalized patient must be transferred to a facility for processing before being returned for administration, all of which takes time and costs money.

In-hospital production is emerging as a viable alternative, which suggests a new generation of automated cell processing technologies could simplify and reduce the cost of making these innovative cures.

Stephan Kadauke, MD, PhD, assistant professor of clinical pathology and laboratory medicine at the University of Pennsylvania’s Perelman School of Medicine, calls these bedside, automated cell processing systems, “GMP-in-a-box.”

“Good manufacturing practice in a box essentially condenses the complex cell therapy manufacturing process into a more compact and automated system that can be housed within a hospital,” he says. “This not only automates an error-prone manual process but also eliminates the need to send cellular materials to centralized manufacturing facilities. We found that this can reduce the cost associated with delivery of novel cell therapies like CAR-T cells to patients. So the advantage is not just in cost, speed, and quality control, but also in patient access.”

Minimizing operator handling

In the study, Kadauke and co-authors looked at a range of in-hospital cell therapy production technologies and found that, although the platforms differ, all of them are designed to link multiple production steps while minimizing operator handling.

“The currently available systems involve a variety of technologies that handle cell selection, culturing, and quality control. Automation plays a significant role in these processes,” he points out. “The goal is to create a ‘one-stop-shop’ for producing cell therapies. The two most mature platforms are the Miltenyi CliniMACS Prodigy and the Lonza Cocoon. However, others are coming.”

Demand for these systems is likely to increase as healthcare professionals seek to improve access to cell therapies, according to Kadauke.

“In-hospital manufacturing is still relatively novel but is gaining traction. A few pioneering hospitals have already implemented such systems, and we expect to see more widespread adoption as the technology matures, especially in parts of the world that currently do not have access to these therapies.”

In addition, Kadauke predicts biopharmaceutical manufacturers will be interested in GMP-in-a-box systems.

“Biopharmaceutical companies also take advantage of GMP-in-a-Box systems to benefit from cost savings due to automation and standardized workflows, though our article focused on in-hospital applications,” he tells GEN. “A large wave of commercial cell therapy products is expected to hit the market in the next year or so, and products manufactured in-hospital with GMP-in-a-box systems will complement and coexist with current and novel commercial cell therapies.”

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Modeling Water’s Shear Viscosity More Accurately https://www.genengnews.com/topics/bioprocessing/modeling-waters-shear-viscosity-more-accurately/ Wed, 18 Oct 2023 16:00:18 +0000 https://www.genengnews.com/?p=274800 Knowing viscosity differences between water models and actual experiments is important. Most drugs and biological molecules, such as proteins, DNA, and polysaccharides, exist in an aqueous environment. The presence of water molecules around these molecules significantly affects their dynamics and interactions. Therefore, developing more accurate water models and their quality assessments are also important for successful biomolecular simulations and in silico drug design.

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By Gail Dutton

Although water’s shear viscosity is important in accurate molecular dynamics modeling, the results from two popular water models differ from those of actual experiments by as much as 20%. In a recent paper, Tadashi Ando, PhD, associate professor at Tokyo University of Science, compared shear viscosity predictions for the four-point Optimal Point Charge (OPC) and three-point OPC (OPC3) models with results from physical experiments. Temperatures ranged from 273°K to 373°K.

Water viscosity for the OPC and OPC3 water models has not been reported in the literature previously. Yet, they are important when evaluating molecules’ self-diffusion coefficients in an infinite system in comparison to molecular dynamic simulations.

Detailing the results in The Journal of Chemical Physics, Ando reported the OPC and OPC3 models were accurate for temperatures above 310°K. Below that, they “systematically underestimated the shear viscosity.” At temperatures of 273°K and 298°K, the calculated viscosities were, respectively, 20% and 10% lower than the experimental values.

Significantly more accurate

Overall, Ando found OPC and OPC3 were significantly more accurate than other popular water models, such as Transferable Intermolecular Potential three-point (TIP3P) or extended Simple Point Charge (SPC/E) models. Other water models—specifically the TIP4P/2005, TIP4P-FB, and TIP3P-FB—predicted shear viscosity more accurately at temperatures below 293°K.

Knowing viscosity differences between models and the actual experiments is important, Ando tells GEN. “Most drugs and biological molecules, such as proteins, DNA, and polysaccharides, exist in an aqueous environment. The presence of water molecules around these molecules significantly affects their dynamics and interactions. Therefore, developing more accurate water models and their quality assessments are also important for successful biomolecular simulations and in silico drug design.”

The OPC and OPC3 water models are “among the best nonpolarizable water models, accounting for the various static and dynamic properties of water,” he says. However, “Most biomolecular models and their force fields have been developed with older water models. Therefore, simply using the OPC/OPC3 water models with many of the existing biomolecular force fields would not yield satisfactory results.”

Improvements are available. “Recently,” Ando says “AMBER, a well-known molecular simulation software and biomolecular force fields developer, developed a protein force field whose performance is improved by using the OPC water model.” Additional biomolecular force fields are likely to be developed with OPC water models to yield more accurate biomolecular simulations.

Ando’s paper may not have a profound, immediate impact on the industry, he says. Instead, it enables deeper understanding of several of the most popular water models so biopharmaceutical manufacturers can select the most appropriate for their biomolecular simulations.

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Analytical Technologies Evolve with Cell Therapies https://www.genengnews.com/topics/bioprocessing/analytical-technologies-evolve-with-cell-therapies/ Wed, 18 Oct 2023 16:00:00 +0000 https://www.genengnews.com/?p=274921 In-process analytics and artificial intelligence could help to better understand process deviations, reducing the number of failed lots. It will require the integration of a tremendous amount of data and analytics, especially for treatments that are lifesaving, such as CAR-T, where the patient may die if they don’t receive the product. Analytics could also be used to personalize medicines to the characteristics of the patient.

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By Vivienne Raper, PhD

Analytical techniques for cell counting and surface marker analyses are improving to meet the needs of cell therapy developers; That’s the view of Lara Silverman, PhD, principal consultant at LIS BioConsulting.

According to Silverman, the growth in advanced therapies is leading to analytical techniques for cell counting beyond, for example, the hemocytometer.

“The analytical space was stagnant, but it’s starting to change because of developments in the bioprocessing world,” Silverman explains. “It’s no longer enough to take the binary approach of knowing if cells are alive or dead. You need to know what cells are doing and how they’re responding to a process.”

Companies might need to know whether cells are metabolically active, alive but no longer expressing a therapeutic marker, or alive but in apotheosis. Although the field is developing techniques for cell counting and identifying surface markers, Silverman says there’s still a delay in the development of new potency assays.

“That might be the reality of our industry [… as] a lot of companies keep their potency assays private because they take so long to develop,” she continues. “But there aren’t yet any ground-breaking discoveries or companies that can consistently support a diverse array of potency assays to streamline [analytics for therapy developers].”

Understanding process deviations

Going forwards, Silverman sees in-process analytics and artificial intelligence as helping to better understand process deviations, reducing the number of failed lots.

“It will require the integration of a tremendous amount of data and analytics, especially for treatments that are lifesaving, such as CAR-T, where the patient may die if they don’t receive the product,” she says.

Analytics could also be used to personalize medicines to the characteristics of the patient, although Silverman believes this may be some time away. “It’s really exciting, but I think the industry is a little scared to dip their toes into it because advanced therapy manufacturers are already challenging the FDA with their drug products.”

Silverman also sees new analytical instruments, such as the Accellix benchtop flow cytometer, as aiding the trend towards decentralized manufacturing.

“Flow cytometry has changed little in many decades. It’s extremely time-consuming and requires manual handling,” she says. “With the Accellix system, you just load your cells into a plastic cartridge that has a specific set of surface markers associated with it, and pop it into a tiny machine, so it’s something that could go on the manufacturing floor rather than in a QC lab.”

Silverman also thinks other instruments, such as the Dynex system for fully-automated ELISA testing, could aid decentralized manufacturing by reducing human error between testing sites. 

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Integrated DNA Technologies Opens Therapeutic Manufacturing Facility https://www.genengnews.com/topics/bioprocessing/integrated-dna-technologies-opens-therapeutic-manufacturing-facility/ Tue, 17 Oct 2023 12:30:12 +0000 https://www.genengnews.com/?p=274763 The 41,000-ft2-site will produce cGMP cell and gene therapy reagents, including single guide RNAs (sgRNAs) and donor oligos for homology-directed repair (HDR) with additional offerings to follow. These new capabilities and offerings will be supported with comprehensive documentation and testing, a support team, and regulatory guidance to help accelerate researchers’ path to the clinic, according to Demaris Mills, president of Integrated DNA Technologies.

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Integrated DNA Technologies (IDT) opened its new therapeutic oligonucleotide manufacturing facility in Coralville, IA. The event marks the 35-year-old company’s entrance into the therapeutics space. It also enables IDT to manufacture products for research use all the way through to current good manufacturing practice (cGMP) grade cell and gene therapy reagents to provide researchers with a single partner.

The 41,000-ft2-site will produce cGMP cell and gene therapy reagents, including single guide RNAs (sgRNAs) and donor oligos for homology-directed repair (HDR) with additional offerings to follow. These new capabilities and offerings will be supported with comprehensive documentation and testing, a support team, and regulatory guidance to help accelerate researchers’ path to the clinic, according to Demaris Mills, president of IDT.

“An increasing number of customers are seeking out IDT as a trusted partner for their CRISPR genome editing needs and are asking us to be the provider that can help them bridge the gap from lab to clinic,” said Mills. “Now, with our new cGMP manufacturing facility, IDT can provide a complete CRISPR workflow—from design to analysis—that supports cell and gene therapy developers in all stages of therapeutic development, with the same support and expertise they have come to know from IDT. These new manufacturing capabilities, which have been informed by our decades of oligonucleotide synthesis manufacturing expertise, evolves IDT’s business model from Research Use Only to cGMP, and enables us to help more people.”

“The future of genomic medicine hinges on the industrialization of biology to make life-saving therapies more accessible to people,” added Chris Riley, Danaher VP and group executive. “As a pioneer in genome editing, IDT’s continued investments will enable customers to rapidly move from clinical development to commercialization. This new facility is another significant milestone in IDT’s innovation journey, one we envision will have a profound impact in genomic medicine for years to come.”

The therapeutic oligo manufacturing facility features ISO 8 cleanrooms, purification suites, chemical distribution and storage rooms, quality control labs, analytical lab space for product testing, ancillary and office spaces, and shell space for future expansion. Manufacturing is performed in accordance with ICH Q7 cGMP standards for consistent and reliable quality. The controlled-access building features environmental controls for temperature, humidity, and air pressure throughout, supported by an environmental program and continuous monitoring system

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Improving Tuberculosis Vaccines Using Immune CD8+ Lymphocytes and IL-15 https://www.genengnews.com/topics/infectious-diseases/improving-tuberculosis-using-immune-cells/ Mon, 16 Oct 2023 19:20:02 +0000 https://www.genengnews.com/?p=274743 Researchers tracked lineages of bacterial granulomas that formed over the course of the disease. In animals lacking innate CD8+ cells, more bacterial dissemination across lungs and lymph nodes were identified, suggesting that innate CD8+ cells create a bottleneck, preventing bacteria from establishing infection. In monkeys with depleted innate CD8+ cells, other immune cells tried to take over the function of fast responders, probably responding to IL-15.

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Researchers from the University of Pittsburgh Center for Vaccine Research report that innate CD8+ lymphocytes are essential for curbing tuberculosis (TB) the disease. They also discovered that Interleukin-15 plays an important role in infection control and could potentially be used to boost the efficacy of existing and future TB vaccines. The team’s study appears in the Journal of Experimental Medicine.

“The functional role of CD8+ lymphocytes in tuberculosis remains poorly understood. We depleted innate and/or adaptive CD8+ lymphocytes in macaques and showed that loss of all CD8α+ cells (using anti-CD8α antibody) significantly impaired early control of Mycobacterium tuberculosis (Mtb) infection, leading to increased granulomas, lung inflammation, and bacterial burden,” wrote the investigators.

“Analysis of barcoded Mtb from infected macaques demonstrated that depletion of all CD8+ lymphocytes allowed increased establishment of Mtb in lungs and dissemination within lungs and to lymph nodes, while depletion of only adaptive CD8+ T cells (with anti-CD8β antibody) worsened bacterial control in lymph nodes.

“Flow cytometry and single-cell RNA sequencing revealed polyfunctional cytotoxic CD8+ lymphocytes in control granulomas, while CD8-depleted animals were unexpectedly enriched in CD4 and γδ T cells adopting incomplete cytotoxic signatures. Ligand-receptor analyzes identified IL-15 signaling in granulomas as a driver of cytotoxic T cells. These data support that CD8+ lymphocytes are required for early protection against Mtb and suggest polyfunctional cytotoxic responses as a vaccine target.

researcher
JoAnne Flynn, PhD, University of Pittsburgh

“This is an unusual finding,” said senior author JoAnne Flynn, PhD, distinguished professor and chair of microbiology and molecular genetics at Pitt. “No one before us has shown that CD8+ lymphocytes make a difference early in the infection in a translatable nonhuman primate model, but our findings suggest that these innate immune cell populations are actually playing an important role in restraining the initial infection.”

Two phases

The immune response over the course of tuberculosis infection has two phases. The first six weeks after the infection are characterized by the influx of quick-acting immune cells that rush to the site of infection, be that the airways or the lung, to kill the bug and limit the damage quickly, by all means necessary.

Unlike the early innate immune response, the adaptive immune response that emerges after eight to 10 weeks of infection is more fine-tuned and aimed at precisely targeting the specific infection-causing pathogen and killing it as efficiently as possible.

In general, the exact dynamics of the immune response in tuberculosis, and the role of fast-acting CD8+ lymphocytes was unclear.

Flynn and her team found that the infection was developing a lot faster and spreading further in macaque monkeys whose innate CD8+ cells were depleted than in monkeys whose total CD8+ T cell population was intact, or whose adaptive CD8+ T cells were removed, suggesting that innate CD8+ cells play a crucial role in limiting the infection in its early stages.

lung x ray
Pulmonary Tuberculosis. Chest X-ray shows interstitial infiltration at left upper lung due to Mycobacterium Tuberculosis infection. [Stockdevil/Getty Images]
Using bacterium barcoding, researchers tracked the lineages of bacterial granulomas that formed over the course of the disease. In animals lacking innate CD8+ cells, researchers identified more bacterial dissemination across lungs and lymph nodes, suggesting that innate CD8+ cells create a bottleneck, preventing bacteria from establishing active infection.

The scientists found that in monkeys with depleted innate CD8+ cells, other immune cells tried to take over the function of fast responders, probably in response to IL-15. But because those cells lack the natural machinery that would enable them to deliver molecules that could kill the bacterium, the infection-clearing immune response was incomplete.

As a next step in their research, scientists are studying whether IL-15 administered together with an existing TB vaccine can increase protection and make the vaccine more effective.

The study was a collaboration between Flynn’s lab and Philana Ling Lin, MD, of the UMPC Children’s Hospital of Pittsburgh, Alex Shalek, PhD, of MIT, and Sarah Fortune, MD, of Harvard University.

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Icahn Mount Sinai and UC San Diego to Establish a Data Integration Hub https://www.genengnews.com/topics/artificial-intelligence/icahn-mount-sinai-and-uc-san-diego-to-establish-a-data-integration-hub/ Wed, 11 Oct 2023 20:29:30 +0000 https://www.genengnews.com/?p=274487 The NIH created The Common Fund Data Ecosystem program to enhance the findability, accessibility, interoperability, and reusability of data generated by Common Fund programs to ensure adherence to the FAIR guiding principles for scientific data. Researchers can explore NIH Common Fund-produced datasets to facilitate new biomedical discoveries and will enable scientists to search across Common Fund-produced datasets to ask complex questions to catalyze new biomedical discoveries.

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Scientists at the Icahn School of Medicine at Mount Sinai and the University of California San Diego received an $8.5 million grant to create a data integration hub aimed at accelerating novel therapeutics and cures for diseases within initiatives supported by the NIH Common Fund.

The NIH created The Common Fund Data Ecosystem (CFDE) program to enhance the findability, accessibility, interoperability, and reusability of data generated by NIH Common Fund programs to ensure adherence to the FAIR guiding principles for scientific data. Researchers can efficiently explore NIH Common Fund-produced datasets to facilitate new biomedical discoveries and will enable scientists to search across Common Fund-produced datasets to ask complex scientific and clinical questions to catalyze new biomedical discoveries, according to an Icahn Mount Sinai spokesperson.

gene sets
Two-dimensional projection of ~620,000 gene sets collected from many related studies, experiments, and projects. [Credit: Lab of Avi Ma’ayan, PhD, Icahn Mount Sinai]
Building on the successes of the pilot phase of the CFDE program, and with a five-year investment of $17 million, the NIH has established two new centers: the CFDE Data Resource Center and the CFDE Knowledge Center. Investigators from Icahn Mount Sinai and the UC-San Diego were selected to lead the CFDE Data Resource Center, and investigators from the Broad Institute of MIT and Harvard were awarded the CFDE Knowledge Center.

“By integrating data from various omics technologies and by making these datasets readily available for analysis and visualization with artificial intelligence and machine learning, many discoveries can emerge,” says the Contact Principal Investigator of the CFDE Data Resource Center, Avi Ma’ayan, PhD, director of the Mount Sinai Center for Bioinformatics and professor of pharmacological sciences, and artificial intelligence and human health. “We are delighted that the NIH has recognized our past contributions to the CFDE, the library of integrated cellular-based signatures (LINCS), and the illuminating the druggable genome (IDG) Common Fund programs and trusts us to lead this new effort.”

Unique opportunity

“This is a unique opportunity to enable a biomedical researcher to make innovative discoveries through full utilization of the data that has emerged from the large investments the National Institutes of Health have made under the aegis of the NIH Common Fund,” adds Principal Investigator of the CFDE Data Resource Center, Shankar Subramaniam, PhD. Subramaniam, the Joan and Irwin Endowed Chair of Bioengineering and Systems Biology at UC San Diego. Subramaniam is the PI of the NIH Common Fund Metabolomics Project.

Currently, most Common Fund datasets are dispersed across distinct data portals, resulting in underutilization due to the absence of standardized community practices and shared data processing protocols, notes Ma’ayan. By enabling seamless discovery of datasets across the Common Fund data, uniformly processing the data, and better combining data from different programs, the investigators anticipate the emergence of synergistic discoveries, he adds.

By working with the Common Fund data coordination centers, the Data Resource Center and Knowledge Center are expected to produce highly valuable computational resources for the entire field of biomedical research, continues Ma’ayan.

“As one example, by integrating exercise-induced gene expression changes from the Common Fund MoTRPAC program, tissue expression data from the GTEx Common Fund program, and drug response data from the LINCS Common Fund program, we can discover new drug candidates and potential treatment targets for muscular dystrophies,” he says.

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