Gene Editing in 3D Patient-Derived Tumor Organoids, Machine Learning Model As Diabetes Prevention Tool, More

December 27, 2022 | A novel mechanism for platelet activation in pathogenic blood clotting is also believed to limit inflammation during sepsis; supercomputing and AI resources apply large language models to track how a virus mutates into more dangerous or transmissible variants; Amazon Web Services to create, fund, and build 10 successful start-up companies based out of UNC-Chapel Hill; and more. 

The Global Biodata Coalition has announced that the Mouse Genome Database (MGD)—hosted at The Jackson Laboratory's Bar Harbor campus—will be included in the first list of Global Core Biodata Resources (GCBRs), a collection of 37 resources whose sustainability is critical to life science and biomedical research worldwide. A key property of the GCBRs is that their data is available openly and can be accessed and used without restriction by researchers worldwide. MGD is the authoritative source of official nomenclature for mouse genes, strains, standard annotations of mouse gene function, and phenotypes. This first set of GCBRs was selected through a rigorous two-stage process that included a panel of more than 50 independent expert reviewers. Press release. 

The Wyss Institute for Biologically Inspired Engineering at Harvard University and EnPlusOne Biosciences announced that the startup company signed a worldwide, exclusive licensing agreement with Harvard’s Office of Technology Development that grants EnPlusOne Bio the rights to commercialize a novel, controlled enzymatic RNA oligonucleotide synthesis technology. The “ezRNA” platform technology was invented and advanced by Wyss Core Faculty member George Church, Ph.D., and an expert team of biologists, chemists, and life science entrepreneurs at the Wyss Institute. EnPlusOne Bio aims to overcome current challenges in manufacturing RNA therapeutics by leveraging a toolbox of proprietary enzymes and nucleic acid building blocks. These range from the efficient synthesis of long RNA sequences (>120 nucleotides) to the installation of therapeutic nucleic acid modifications for stabilization and delivery purposes. Press release. 

Research on antibiotic resistance will broaden significantly when the Center for Antibiotic Resistance Research (CARe) in Gothenburg expands. Bacterial resistance to antibiotics is one of the most serious global health threats. CARe at the University of Gothenburg has been researching to address this complex challenge since 2016. From January 1, 2023, CARe will comprise nearly 150 researchers from more than 20 departments across the academic partners. Some ten active research groups will be active in CARe after the expansion. Press release. 

The Lee Kong Chian School of Medicine at Nanyang Technological University, Singapore, in collaboration with other healthcare institutions, has embarked on a landmark comprehensive health study of 100,000 Singaporeans to identify the social, environmental, lifestyle, and genetic factors associated with diseases prevalent in Singapore, such as diabetes, hypertension, and cancer. Throughout the study, SG100K participants will be monitored for their long-term health outcomes through various approaches, including electronic medical records, disease registries, and invitations for further follow-up. SG100K will also analyze blood samples to assess the population's genomic and other relevant molecular variations. Participants will be offered a detailed health report, which they can use for discussion with their doctors at no charge. Press release. 

Florida International University (FIU) researchers have moved a step closer to producing synthetic arsenic-based drugs in their quest to solve an urgent worldwide health problem—the growing number of infections that have become antibiotic-resistant. The FIU Herbert Wertheim College of Medicine and the FIU College of Arts, Sciences, and Education teams have been awarded a U.S. patent for developing chemically synthesizing arsinothricin methods, a new arsenic-based antibiotic. While the group’s research has progressed steadily, they hope to gain the interest of angel investors and pharmaceutical companies that see the potential in their work. Press release. 

Clinithink partnered with AstraZeneca Oncology UK in a new project to find patients with early-stage lung cancer when treatment can be more effective. The project aims to flag patients that could benefit from lung disease screening, leading to earlier diagnosis of the disease, improved patient outcomes, and reduced costs for the NHS. Using AI-based technology, the first stage of the project is a retrospective analysis of patients’ unstructured electronic medical records that will test whether it is possible and cost-effective to use the AI technology—machine learning and natural language processing—to identify both symptomatic and asymptomatic patients who are in early stages of the disease. The outputs will then be used to develop predictive models that flag high-risk individuals at a much earlier, more treatable stage of disease, improving survival rates and driving down the intensity of treatment needed. If successful, the team will develop a prospective model in mid-2023 to prove the validity of the approach in the real world. Press release. 

PhoreMost and ThinkCyte K.K. announced a strategic research partnership to advance modern phenotypic drug screening using artificial intelligence. The partnership leverages both companies’ distinctive technologies in high-throughput drug discovery, PhoreMost’s next-generation phenotypic screening platform, SITESEEKER, and ThinkCyte’s AI-driven cell characterization and sorting platform, Ghost Cytometry, to develop differentiated therapies for a range of diseases with an unmet clinical need. By combining SITESEEKER to identify novel druggable targets with Ghost Cytometry to identify subtle phenotypic changes in living cells, the partnership aims to develop a unique approach to high-content phenotypic screening. The research partnership will drive ThinkCyte deeper into early drug discovery and contribute to PhoreMost’s mission of “Drugging the Undruggable.” Press release. 

PrecisionLife Limited announced that it has entered into a multi-target discovery and validation partnership with Ono Pharmaceutical Co. The R&D collaboration will leverage PrecisionLife’s combinatorial analytics-generated insights to identify novel therapeutic targets and patient stratification biomarkers in central nervous system disorders for development by Ono. PrecisionLife will use its considerable drug discovery expertise to provide Ono with a clear rationale for selecting targets with genetic validation and mechanistic hypotheses, preclinical validation, and patient stratification biomarkers to optimize the clinical development of the assets. Ono will select targets from PrecisionLife’s recommendations and acquire the worldwide rights to develop and commercialize a pharmaceutical product acting on the target. Press release. 

Researchers from the University of Birmingham, UK—who identified a novel mechanism for platelet activation in pathogenic blood clotting (thrombosis)—are now focusing on sepsis. The Birmingham Platelet Group determined that the previously unknown axis comprises platelet receptor glycoprotein I alpha (GPIbα) and an anti-microbial protein S100A8/A9, released from activated immune cells (Blood, DOI: 10.1182/blood.2021014966). The researchers believe this novel mechanism may be relevant in thrombosis observed under chronic inflammatory conditions and acute infections and believe that the interaction of S100A8/A9 with multiple receptors makes it an exciting target to limit both clotting and inflammation during sepsis. Press release. 

Crown Bioscience and ERS Genomics Limited have signed a global license agreement to access the foundational CRISPR/Cas9 patent portfolio held by ERS, which provides the company full license to operate globally using CRISPR/Cas9 for gene editing. With this new agreement, Crown Bioscience will expand its gene editing capabilities and investigate the prospect of gene editing in 3D patient-derived tumor organoid models. The agreement also allows the company to develop additional unique and relevant preclinical tools in 3D for higher throughput screens, with the option to add matched in vivo models downstream for translational studies. Press release. 

Vizgen announced the launch of its highly anticipated MERSCOPE Formalin-Fixed Paraffin-Embedded (FFPE) Solution, enabling high multiplexing, high-resolution single-cell, and spatial genomics analysis of FFPE samples. The MERSCOPE FFPE Solution includes new sample preparation kits, user-friendly workflow, and updated, innovative segmentation software to enable researchers to process, image, and analyze FFPE samples effectively. In contrast to other spatial genomics platforms, MERSCOPE FFPE data is generated using peer-reviewed and validated MERFISH technology, providing high accuracy with bulk RNA-sequencing data across the entire expression profile for accurate detection of high, middle, and low abundance genes. Together with its impressive reproducibility between matched fresh frozen and FFPE tissue samples, the MERSCOPE FFPE solution delivers biologically impactful data. Press release. 

Many companies seeking strong starts to 2023 are planning to use AI and accelerated computing to drive growth while saving costs. To support these early adopters and those just beginning their AI journey, NVIDIA has announced a new version of its NVIDIA AI Enterprise software suite to support businesses worldwide across a wide range of domain and industry-specific workloads. NVIDIA AI Enterprise 3.0 will introduce workflows for contact center intelligent virtual assistants, audio transcription, and digital fingerprinting for cybersecurity. Expected to be available later this month, NVIDIA AI Enterprise 3.0 also expands support for more than 50 NVIDIA AI software frameworks and pre-trained models available on the NVIDIA NGC software catalog, supercharging and simplifying AI deployments for organizations globally. Press release. 

BGI Genomics and the University of Pécs (UP) agreed to launch a joint laboratory in Hungary as part of the cooperation agreement signed between BGI Group, the parent company of BGI Genomics, and the University. This world-class facility will accelerate the development of genomic sequencing and clinical diagnostic services while strengthening BGI Genomics and the UP's leadership in genomics, bioinformatics, reproductive health, and precision medicine in the Central and Eastern European region. BGI Genomics provides training and technical support at this joint laboratory for researchers to leverage next-generation sequencing platforms to develop and deliver world-leading genome sequencing and clinical diagnostic services. Both parties seek to advance public health screening programs and integrate monitoring strategies into managing individuals' health to improve health awareness and quality of life. Press release. 

The Center for the Advancement of Science in Space and the U.S. National Science Foundation (NSF) opened a joint solicitation seeking projects that use the International Space Station (ISS) National Laboratory to advance tissue engineering and mechanobiology research. Through this solicitation, the NSF will provide up to $1.6 million in funding for multiple projects to launch to the space station under the sponsorship of the ISS National Lab. This joint solicitation aims to further drug discovery and therapeutic development through space-based research. The deadline to submit a Feasibility Review Form is January 9, 2023. Only investigators whose concept passes the Feasibility Review Form step will be invited to submit a full proposal. NSF will close this solicitation on March 6, 2023. To learn more about the benefits of conducting research leveraging the ISS National Lab, please visit www.ISSNationalLab.org. Press release. 

Scientists at Klick Applied Sciences have discovered a way to transform a continuous glucose monitor (CGM) into a powerful diabetes screening and prevention tool using artificial intelligence. The team revealed how they used machine learning and just 12 hours of data from CGMs to determine whether a patient was prediabetic or diabetic. They discovered their 12-hour model correctly identified two-thirds of patients with prediabetes and showed high accuracy in identifying healthy patients and those with Type 2 diabetes. Their study—published in Nature (DOI: 10.1038/s41746-020-0283-x)—was based on mathematical modeling to determine how some underlying changes in glucose regulation cause diabetes. Press release. 

Critical Path Institute (C-Path) and Ultragenyx Pharmaceutical announced a data-sharing agreement to incorporate rare disease patient data into C-Path’s Rare Disease Cures Accelerator-Data and Analytics Platform (RDCA-DAP). RDCA-DAP provides a centralized and standardized infrastructure to support and accelerate rare disease characterization targeted for clinical development. It includes a robust, integrated database and analytics hub that aggregates rare disease data from various sources and efficiently and effectively interrogates it. RDCA-DAP continues to enrich its database—including muscular and neuromuscular disorders—with more than 66 datasets spanning 25 different diseases. Ultragenyx and RDCA-DAP have a shared mission to accelerate the development of medical products and effective treatments for rare diseases, offering patients and families hope for the future. Press release 

Jumpcode Genomics announced a partnership with 10x Genomics to integrate the Jumpcode Single Cell RNA Boost Kit with the 10x Genomics Chromium Single Cell Gene Expression platform. An abundance of uninformative sequences can obscure valuable next-gen sequencing (NGS) data. Jumpcode’s CRISPRclean technology is changing that. Leveraging Cas9 and specifically designed guides, the Single Cell RNA Boost Kit degrades abundant, uninformative sequences in NGS libraries, redistributing 50% of sequencing clusters to unique biologically relevant transcripts. Jumpcode’s solution has now been validated with 10x Genomics’ Chromium Single Cell 3’ Gene Expression microfluidic platform, which enables researchers to scale experiments for single-cell analysis. Combining these two technologies empowers scientists to cut through sequencing noise and boost usable data. Press release. 

Queen Mary University of London has become the first university outside North America to acquire a Cell DIVE imager. The Cell DIVE provides multiplexed imaging of tissue sections, enables high-dimensional tissue imaging for quantitative analysis of at least 60 biomarkers, and visualizes the inner workings of single cells on a previously unattainable level. What makes this technology platform significant is the integration of biology, precision imaging, and sophisticated analysis software to enable deep insights at the single-cell level. As part of its 2030 strategy, the University provides a world-class virtual and physical research infrastructure. Queen Mary has been ranked joint seventh in the UK for the quality of its research—according to the Research Excellence Framework 2021—and 92% of Queen Mary’s research was assessed as internationally excellent or world-leading according to the REF21 results. Press release. 

The University of North Carolina at Chapel Hill, through the Eshelman Institute for Innovation, announced a collaboration with Amazon Web Services to build an environment for startup creation that uses cloud technology to translate UNC-Chapel Hill's digital health research expertise into commercialized solutions. The partnership will support 25 projects over three years, aiming to create, fund, and build 10 successful start-up companies based out of UNC-Chapel Hill. The focus is software-forward digital technologies to advance health and wellness, enhance patient and provider experience, and improve healthcare access across five areas: enterprise systems and support, clinician services and support, patient-facing wellness and support, patient-facing diagnostic and monitoring, and patient-facing therapeutic interventions. For more information, visit UNC’s Eshleman Institute for Innovation’s website or contact the team. Press release. 

Scientists from the U.S. Department of Energy’s Argonne National Laboratory and a team of collaborators have won the 2022 Gordon Bell Special Prize for High Performance Computing-Based COVID-19 Research for their new method of quickly identifying how a virus evolves. The researchers who won this year’s prestigious award leveraged powerful supercomputing and AI resources to develop and apply large language models to track how a virus can mutate into more dangerous or transmissible variants. Their paper is the culmination of the team’s findings (bioRxiv, DOI: 10.1101/2022.10.10.511571). Their work resulted in the first genome-scale language model (GenSLM), which is a model that can analyze genes and rapidly identify variants of concern (VOCs). GenSLM is the first whole genome-scale foundation model that can be altered and applied to other prediction tasks similar to VOC identification. Press release.