A deep learning-based model DeepSpCas9 to predict SpCas9 activity

Phys.org | November 22, 2019

In a new report on Science Advances, Hui Kwon Kim and interdisciplinary researchers at the departments of Pharmacology, Electrical and Computer Engineering, Medical Sciences, Nanomedicine and Bioinformatics in the Republic of Korea, evaluated the activities of SpCas9; a bacterial RNA-guided Cas9 endonuclease variant (a bacterial enzyme that cuts DNA for genome editing) from Streptococcus pyogenes. They used a high-throughput approach with 12,832 target sequences based on a human cell library to build a deep learning model and predict the activity of SpCas9. The data contained oligonucleotides (nucleotides or building blocks) containing target sequence pairs and a corresponding guide sequence to encode single-guide RNA (sgRNA), which can direct the Cas9 protein to bind and cleave a specific DNA sequence for genome editing. They implemented deep learning-based training on the large dataset of SpCas9-induced indel (insertion or deletion) frequencies to develop an SpCas9 activity predicting model named DeepSpCas9 now available online. When the team tested the software against independently generated datasets, the results showed high generalization performance, i.e. the model could properly adapt to new, previously unseen data.

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FogPharma Announces $178 Million Series D Financing to Advance Pipeline of First-in-Class Helicon Polypeptide Therapeutics Targeting

FogPharma | November 22, 2022

FogPharma®, a biopharmaceutical company pioneering a new class of precision medicines that could ultimately prove applicable to the vast majority of therapeutic targets, including those previously considered “undruggable,” today announced a $178 Million Series D financing. The financing round includes new investors ARCH Venture Partners, Milky Way Investments and Fidelity Management & Research Company and existing investors VenBio Partners, Deerfield Management, GV, Cormorant Asset Management, funds and accounts advised by T. Rowe Price Associates, Inc., Invus, Farallon Capital Management, HBM Healthcare Investments, Casdin Capital, and PagsGroup, also participated. Proceeds from the Series D financing will be used to advance and accelerate FogPharma’s growing pipeline of hyperstabilized α-helical polypeptide therapeutics, a proprietary new class of drugs designed to overcome the limitations of today’s precision medicines with broad applicability to the vast majority of disease targets and therapeutic areas. FogPharma’s lead Helicon polypeptide development candidate, FOG-001, a first-and-only-in-class direct TCF-blocking β-catenin inhibitor with potential applicability to significant cancer patient populations, is expected to enter clinical development in mid-2023. In addition, FogPharma is advancing other first-in-class programs against important, biologically validated cancer targets that have remained elusive to other approaches including TEAD, NRAS, Pan-KRAS, ERG and Cyclin E1. “FogPharma continues to make rapid progress on our moonshot mission to achieve universal druggability – a world where no targets are off-limits to medicine. We believe that Helicon polypeptides, a compelling new therapeutic modality, represent the future of precision medicine. We are thrilled by the support of our investors and will continue to build our platform capabilities, product pipeline which aims to address a significant percentage of cancer patient populations, and our phenomenal team across all levels as we aim to create one of the most impactful new classes of drugs in history.” Gregory Verdine, Ph.D., founder, chairman and chief executive officer of FogPharma In connection with the Series D Financing, Rick Klausner, M.D., has been appointed to FogPharma’s board of directors. In addition, Dr. Verdine has been appointed as chairman of the board. “The team at FogPharma is building an unprecedented new therapeutic modality and robust pipeline with the potential to make a meaningful difference in the lives of cancer patients,” said Dr. Klausner. “I am excited to join the board of directors and be part of something special – particularly at this important time as FogPharma continues to impressively scale its science, team, operations and infrastructure, with the goal of advancing its first Helicon polypeptide therapeutic into the clinic.” Dr. Klausner is currently the founder and chief scientist of Altos Labs and founder and chairman of Lyell Immunopharma. Dr. Klausner was founder and director of Juno Therapeutics and founder and director of GRAIL. He is also the chairman of Sonoma Biotherapeutics and co-founder and chairman of Lifemine Therapeutics. Previously, Dr. Klausner served as senior vice president, chief medical officer and chief opportunity officer of Illumina Corporation and as executive director for global health for the Bill and Melinda Gates Foundation. Dr. Klausner was appointed by Presidents Clinton and Bush as the eleventh director of the U.S. National Cancer Institute (NCI) between 1995 and 2001. Dr. Klausner served as chief of the Cell Biology and Metabolism Branch of the National Institute of Child Health and Human Development as well as a past president of the American Society of Clinical Investigation. He has served in senior advisory roles to the U.S., Norwegian, Qatari and Indian governments. About FogPharma’s Universal Druggability Platform and Helicon™ Polypeptide Therapeutics Existing drug classes are limited in both reach and applicability, with more than 80% of known human protein disease targets considered “undruggable” because they are beyond the reach of both antibodies and small molecules. FogPharma’s Helicon peptide drug discovery engine integrates directed evolution, proprietary α-helix conformational hyperstabilization chemistry, highly multiplexed drug optimization technology, artificial intelligence including deep learning and machine learning, structure-based drug discovery, cancer genomics and biology, and multiscale manufacturing to rapidly discover Helicon polypeptide therapeutics. This novel therapeutic modality combines the targeting strength and specificity of antibodies with the broad tissue distribution, intracellular target engagement and oral dosing optionality of small molecules to address the limitations of today’s precision medicines and reach the most difficult targets – achieving universal druggability. About FOG-001 FogPharma’s lead Helicon polypeptide development candidate, FOG-001, a first-and-only-in-class direct TCF-blocking β-catenin inhibitor. Dysregulation of the Wnt/β-catenin signaling pathway has been shown to occur in at least 20% of all human cancers. In the U.S. alone, FOG-001 has the potential to become a new treatment option for >1 million patients suffering from a broad range of intractable cancers. In biochemical and cellular studies, FOG-001 has been shown to potently, precisely and selectively disrupt the interaction of β-catenin with its obligate downstream transcription factor, TCF. Preclinical studies have demonstrated the ability of FOG-001 to cause tumor growth inhibition and regression by disrupting β-catenin-dependent signaling. FOG-001 is the inaugural member of FogPharma’s TCF-Catenix family of direct-acting β-catenin antagonists and combines key features that distinguish it from previously reported Wnt/β-catenin pathway modulators: FOG-001 acts inside the cell, where it directly binds the key oncogenic driver β-catenin; and FOG-001 blocks TCF-β-catenin engagement at the most downstream node in the canonical Wnt pathway, thus abrogating the signal transmission mechanism by which most, if not all, known Wnt pathway mutations are believed to drive oncogenesis. About FogPharma FogPharma is a biopharmaceutical company pioneering the discovery and development of Helicon™ polypeptides. Through this novel therapeutic modality, FogPharma aims to address the limitations of existing drug classes and achieve universal druggability – a world where no targets are off-limits to new medicines. Spun out of Harvard University by pioneering academic scientist and successful biotech company builder Dr. Gregory Verdine, FogPharma is advancing a broad pipeline of Helicon polypeptide therapeutics against important and biologically validated cancer targets that have remained elusive to other approaches, with the goal of providing new targeted treatment options for significant cancer patient populations. FogPharma is headquartered in Cambridge, Mass., and has raised more than $360 million to date from leading life sciences investors.

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INDUSTRIAL IMPACT

IPA’s Subsidiary BioStrand and BriaCell Announce Artificial Intelligence Collaboration and License Agreement

BriaCell Therapeutics Corp. | December 01, 2022

IPA an advanced biotherapeutic research and technology company, announced that BioStrand BV an AI in silico discovery subsidiary of IPA, has entered into a research collaboration and license agreement with BriaCell Therapeutics Corp. a clinical-stage biotechnology company specializing in targeted immunotherapies for cancer. The collaboration will leverage BioStrand’s LENSai™ software, built upon IPA’s proprietary HYFT™ Universal Fingerprint™ technologies, and will focus on in silico antibody discovery to generate relevant clinical molecules for potential development. Under the terms of the Agreement, BioStrand and BriaCell will collaborate on the design, discovery, and development of anti-cancer antibodies. Upon successful antibody discovery, BioStrand will receive an upfront payment of US$500,000, and will be eligible to receive future success-based development milestones, including those for the submission of Investigational New Drugs clinical milestone payments, and commercial royalties on net sales of products. Further terms are not disclosed. “We are very excited to begin this program with BriaCell and apply our technology to the development of biologics that may have a huge clinical impact. Shortening timelines, while also integrating as much information as possible upstream to improve the efficiency of the process, is extremely important in the development of highly targeted therapies. It is a step towards realizing our long-term vision of significantly advancing precision medicine.” Dr. Ingrid Brands, General Manager and co-founder of BioStrand “We believe that BioStrand’s revolutionary AI-powered technology, combined with its cutting-edge protein engineering platform, will allow us to design and discover potent anti-cancer therapeutics,” stated Miguel A. Lopez-Lago, PhD, Chief Scientific Officer of BriaCell. “This approach would complement BriaCell’s current immunotherapy pipeline of innovative anti-cancer therapeutics.” About BriaCell Therapeutics Corp. BriaCell is an immuno-oncology-focused biotechnology company developing targeted and effective approaches for the management of cancer. ImmunoPrecise Antibodies Ltd. ImmunoPrecise Antibodies Ltd. has several subsidiaries in North America and Europe including entities such as Talem Therapeutics LLC, Biostrand BV, ImmunoPrecise Antibodies Ltd. and ImmunoPrecise Antibodies B.V. The IPA Family is a biotherapeutic research and technology group that leverages systems biology, multi-omics modelling and complex artificial intelligence systems to support its proprietary technologies in bioplatform-based antibody discovery. Services include highly specialized, full-continuum therapeutic biologics discovery, development, and out-licensing to support its business partners in their quest to discover and develop novel biologics against the most challenging targets.

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Athersys Amends Securities Purchase Agreement in Connection with Recent Registered Direct Offering

Athersys, Inc. | September 26, 2022

Athersys, Inc. a regenerative medicine company developing MultiStem® for critical care indications, announced that it has entered into amended agreements to extend the exercise period of the warrants that were issued as part of a registered direct offering that closed on August 17, 2022, among other changes, and to issue additional warrants to the same warrant holder, a healthcare-focused U.S. institutional investor. The Purchase Agreement contains certain restrictions that, subject to certain exceptions, prohibit the Company from issuing its common stock in certain variable rate transactions for a period of 180 days following the Closing Date. The Purchase Agreement also gives the Purchasers the right to participate in certain future offerings of the Company in an amount of up to 30 percent in the aggregate of any offered securities during the 12 months following the Closing Date. On September 22, 2022, the Company entered into an amendment to the Purchase Agreement with the Purchasers to, among other things, (i) extend the exercise period of the Initial Warrants from five years to seven years after the six-month anniversary of the Closing Date (the “Warrant Amendment”), (ii) reduce the Standstill Period from 180 days to 150 days following the Closing Date, (iii) reduce the term and amount of the Participation Right from twelve months to six months following the Closing Date and from 30 percent to 20 percent in the aggregate of any offered securities, respectively, and (iv) require the Purchasers, subject to certain conditions, to participate in the event the Company proposes to offer and sell shares of offered securities during the six months following the Closing Date to investors primarily for capital raising purposes. In return, Athersys issued to the same warrant holder additional warrants that are exercisable for an aggregate of 2,000,000 shares of common stock and have an exercise price of $6.3850 for a seven-year period after the six-month anniversary of the date of issuance. A more detailed discussion of the amendments is contained in a Current Report that Athersys filed on September 22, 2022 with the U.S. Securities and Exchange Commission on Form 8-K. “We are pleased to have entered into this amendment with our new major investor which provides more financial flexibility going forward as well as a commitment for the investor that recently invested $12 million in Athersys to participate in future financings if requested. As Athersys continues to pursue licensing and other business development opportunities for our proprietary technology this amendment can help facilitate future transactions with financial and strategic investors. We are fortunate to have established a strong relationship with a prominent healthcare focused institutional investor that embraces the value of our MultiStem cell therapy and is responsive to our priorities,” Dan Camardo, Chief Executive Officer of Athersys “I am also pleased with progress we’ve made in our business transformation and I look forward to updating shareholders during a conference call to be held the week of October 3rd,” he added. Athersys intends to issue a separate news release that will provide further information on the date and time of the call, as well as instructions regarding how to participate. About MultiStem® MultiStem® cell therapy is a patented regenerative medicine product in clinical development that has shown the ability to promote tissue repair and healing in a variety of ways, such as through the production of therapeutic factors in response to signals of inflammation and tissue damage. MultiStem therapy’s potential for multidimensional therapeutic impact distinguishes it from traditional biopharmaceutical therapies focused on a single mechanism of benefit. The therapy represents a unique “off-the-shelf” stem cell product that can be manufactured in a scalable manner, may be stored for years in frozen form, and is administered without tissue matching or the need for immune suppression. Based upon its efficacy profile, its novel mechanisms of action, and a favorable and consistent tolerability demonstrated in clinical studies, we believe that MultiStem therapy could provide a meaningful benefit to patients, including those suffering from serious diseases and conditions with unmet medical need. About Athersys Athersys is a biotechnology company engaged in the discovery and development of therapeutic product candidates designed to extend and enhance the quality of human life. The Company is developing its MultiStem® cell therapy product, a patented, adult-derived “off-the-shelf” stem cell product, initially for disease indications in the neurological, inflammatory and immune, and other critical care indications and has several ongoing clinical trials evaluating this potential regenerative medicine product. Athersys has forged strategic partnerships and a broad network of collaborations to further advance MultiStem cell therapy toward commercialization.

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