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GARFIELD classifies disease-relevant changes in the genome

Medical Xpress | January 30, 2019

Researchers at the Wellcome Sanger Institute and EMBL's European Bioinformatics Institute (EMBL-EBI) have developed a new approach to understanding the functional effects of genetic variations associated with a disease, even if they aren't located in a gene. Using this approach could help scientists uncover previously unknown mechanisms that control gene activity and determine whether cell work normally or, in the case of genetic diseases, the cells malfunction. This knowledge will help drive new research and could identify new targets for drug development.
The tool, called GARFIELD, uses a computational approach known as functional enrichment. This approach combines the positions on the genome of disease-associated DNA changes with information on the role of those regions. In this way, the system highlights those variations that are known to produce changes in the activity of genes that are relevant to the disease being studied. GARFIELD has been designed to take into account the major factors that could confuse the results of a study and can include weak disease associations to increase its power for insight. Because of these measures, the system provides the widest information on the largest number of disease associations.

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Gene and cell therapy analytical and development methods

In the three decades that have passed since the approval of the first gene therapy in 1990, these revolutionary medicines have changed the lives of patients all over the world1.

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Spotlight

Gene and cell therapy analytical and development methods

In the three decades that have passed since the approval of the first gene therapy in 1990, these revolutionary medicines have changed the lives of patients all over the world1.

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Twist Bioscience Launches Portfolio of RNA Sequencing Tools

Businesswire | May 23, 2023

Twist Bioscience Corporation a company enabling customers to succeed through its offering of high-quality synthetic DNA using its silicon platform, today announced the launch of a portfolio of RNA sequencing tools, which includes the Twist RNA Exome, Twist RNA Library Prep Kit and the Twist Ribosomal RNA (rRNA) & Hemoglobin (Globin) Depletion Kit, as well as custom target enrichment capabilities for RNA and whole transcriptome sequencing. This comprehensive suite of RNA tools can enable targeted or whole transcriptome research across fields including precision medicine, biomarker discovery and immuno-oncology research. “Twist’s RNA sequencing portfolio builds on our established NGS capabilities in genomic sequencing and methylation detection and expands into gene expression analysis, opening a new and significant market for Twist,” said Emily M. Leproust, Ph.D., CEO and co-founder of Twist Bioscience. “This offering allows our customers to leverage Twist’s leading target enrichment platform to discover and resolve low abundance RNA transcripts in the human transcriptome. Our RNA sequencing workflows are designed specifically for challenging samples. By enriching relevant transcripts, we can enable researchers to get high-quality data from a range of sample types, including damaged RNA.” Unlike the genome, which is relatively static, the transcriptome changes over time in response to varying disease states and drug therapies. Gene expression levels also differ across tissues and cell types. To fully understand this dynamic quality of RNA, researchers often sequence RNA samples from the same source at multiple time points, incurring additional costs and resource burdens. Each component of the Twist RNA sequencing portfolio is purpose-built to maximize data quality, minimize workflow inefficiency, decrease wasted sequencing reads, and support comprehensive transcriptomic profiling across even low-quality and low-input samples common in oncology. The Twist RNA sequencing portfolio provides end-to-end workflows that can be used to study total RNA and measure the whole transcriptome, protein coding sequences of messenger RNA (mRNA) or custom targets. These products can also be integrated into customers’ existing workflows. Twist RNA sequencing tools enable minimal hands-on time and increase the scale of samples sequenced through utilizing automation. They are compatible with a wide range of sample inputs, including difficult or low-quality samples. RNA panel designs can also now incorporate Twist’s new exon-aware design algorithm, which reduces bias in detection and can provide an important tool for researchers studying rare gene transcripts that drive tumor biology. Twist Targeted RNA Sequencing Workflow Twist target enrichment for RNA leverages the performance, efficiency and sensitivity of Twist target enrichment for sequencing of RNA transcripts of interest across samples and species. It can be used to enrich relevant transcripts with the RNA Exome or in custom RNA panels. Twist RNA Exome The Twist RNA Exome with Twist’s exon-aware design algorithm enables targeted sequencing of the protein coding regions of the human transcriptome without bias toward specific combinations of exons. The Twist RNA Exome covers up to 99.9% of protein coding sequencing in Gencode and RefSeq databases. This coverage, along with the exon-aware design approach, could enable researchers to capture important transcripts including those in low input and degraded samples from formalin fixed paraffin embedded (FFPE) sections. Twist Whole Transcriptome Sequencing Workflow Twist Whole Transcriptome Sequencing can be used to discover novel transcripts, including low expressing genes and novel isoforms. It can be used with a variety of samples including whole blood, fresh and frozen tissue samples and low quality samples, such as FFPE samples. The Twist rRNA & Globin Depletion Kit can be used with this workflow to deplete rRNA and hemoglobin targets so that researchers can study the rest of the transcriptome. The full workflow can be completed in less than five hours with minimal hands-on time. About Twist Bioscience Corporation Twist Bioscience is a leading and rapidly growing synthetic biology and genomics company that has developed a disruptive DNA synthesis platform to industrialize the engineering of biology. The core of the platform is a proprietary technology that pioneers a new method of manufacturing synthetic DNA by “writing” DNA on a silicon chip. Twist is leveraging its unique technology to manufacture a broad range of synthetic DNA-based products, including synthetic genes, tools for next-generation sequencing (NGS) preparation, and antibody libraries for drug discovery and development. Twist is also pursuing longer-term opportunities in digital data storage in DNA and biologics drug discovery. Twist makes products for use across many industries including healthcare, industrial chemicals, agriculture and academic research.

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Cellectis Presents Clinical Data on AMELI-01 and Preclinical Data on Multiplex Engineering for Superior Generation of CAR T-cells at ASGCT 2023

Globenewswire | May 18, 2023

Cellectis a clinical-stage biotechnology company using its pioneering gene-editing platform to develop life-saving cell and gene therapies, today presents clinical data on its Phase 1 AMELI-01 clinical trial (evaluating UCART123) that were unveiled in an oral presentation at the 64th American Society of Hematology (ASH) annual meeting, as well as preclinical data on multiplex engineering for superior generation of CAR T-cells, at the American Society of Gene and Cell Therapy (ASGCT) 2023 Annual Meeting. Preliminary Clinical Data from the AMELI-01 Study Presented at ASH 2022 AMELI-01 is a Phase 1 open-label dose-escalation trial evaluating the safety, tolerability, expansion and preliminary activity of UCART123 given at escalating dose levels after lymphodepletion (LD) with either fludarabine and cyclophosphamide (FC) or FC with alemtuzumab (FCA) in patients with relapsed or refractory acute myeloid leukemia (r/r AML). The oral presentation reviewed preliminary data from patients who received UCART123 at one of the following dose levels: dose level 1 (DL1) 2.5x105 cells/kg; dose level 2 (DL2) 6.25x105 cells/kg; intermediate dose level 2 (DL2i) 1.5x106 cells/kg; or dose level 3 (DL3) 3.30x106 cells/kg after lymphodepletion with FC ([n=8], DL1 – DL3) or FCA ([n=9], DL2 & DL2i). Preliminary Safety Data The FCA LD regimen resulted in robust lymphodepletion for greater than 28 days in all patients. Seven out of nine patients demonstrated UCART123 expansion, with maximum concentration (Cmax) ranging from 13,177 to 330,530 copies/μg DNA, an almost nine-fold increase compared with FC LD, and a significant increase in area under the curve (AUC) (0-28 days) (p=0.04; FC 10.2 vs. FCA 34.9). Cytokine release syndrome (CRS) occurred in eight patients in the FC arm and nine patients in the FCA arm. In the FC arm, one patient experienced Grade 3 immune effector cell-associated neurotoxicity syndrome (ICANS) and two patients experienced Grade 4 protocol-defined dose limiting toxicities (DLTs) secondary to CRS. In the FCA arm, two patients experienced Grade 5 DLTs secondary to CRS. Patient Enrollment in a 2-Dose Regimen Arm Overall, these preliminary data support the continued administration of UCART123 after FCA lymphodepletion in patients with r/r AML. Based on observed UCART123 expansion patterns and cytokine profiles, pursuant to an amended protocol, a second dose of UCART123 is given after 10-14 days to allow for additional UCART123 expansion and clinical activity without the use of additional lymphodepletion. The UCART123 cell expansion from the second dose of UCART123, in the setting of reduced disease burden, is expected to be safe and allow for clearance of residual disease. About Cellectis Cellectis is a clinical-stage biotechnology company using its pioneering gene-editing platform to develop life-saving cell and gene therapies. Cellectis utilizes an allogeneic approach for CAR-T immunotherapies in oncology, pioneering the concept of off-the-shelf and ready-to-use gene-edited CAR T-cells to treat cancer patients, and a platform to make therapeutic gene editing in hemopoietic stem cells for various diseases. As a clinical-stage biopharmaceutical company with over 23 years of experience and expertise in gene editing, Cellectis is developing life-changing product candidates utilizing TALEN®, its gene editing technology, and PulseAgile, its pioneering electroporation system to harness the power of the immune system in order to treat diseases with unmet medical needs. Cellectis’ headquarters are in Paris, France, with locations in New York, New York and Raleigh, North Carolina. Cellectis is listed on the Nasdaq Global Market and on Euronext Growth .

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BenevolentAI Progresses BEN-34712 for the Potential Treatment of ALS into IND-Enabling Studies

Businesswire | June 05, 2023

BenevolentAI, a leader in the development of cutting-edge AI that accelerates biopharma discovery, announces the successful delivery of its pre-clinical candidate for the potential treatment of amyotrophic lateral sclerosis (ALS), BEN-34712. BEN-34712 is an oral, potent and selective brain penetrant RARɑβ (retinoic acid receptor alpha beta) biased agonist and will now enter investigational new drug (IND)-enabling studies. Impaired retinoic acid signalling has been shown to result in neuroinflammation, oxidative stress and mitochondrial dysfunction, all hallmarks of ALS. In preclinical studies conducted by the Company, BEN-34712 was neuroprotective in a patient-derived, disease-relevant in vitro motor neuron/iAstrocyte co-culture model, demonstrating significant efficacy in both sporadic and familial subtypes of ALS. In addition, BEN-34712 has demonstrated both central nervous system (CNS) target engagement and functional protective effects in the SOD1G93A mouse model of ALS after 50-day repeat dosing. BenevolentAI collaborated with the Sheffield Institute for Translational Neuroscience (SITraN) at the University of Sheffield on this programme, utilising their patient-derived motor neuron/iAstrocyte co-culture systems and in vivo model expertise. Anne Phelan, Chief Scientific Officer, BenevolentAI, said: “There remains a significant and urgent need for new and alternative therapies for patients with ALS. We are pleased by the promising advancement of our drug candidate, BEN-34712, towards clinical development, backed by the compelling preclinical data generated by our collaborators at SITraN.” Richard Mead, Senior Lecturer in Translational Neuroscience at SITraN, commented: "ALS patients suffering from this devastating neurodegenerative disease are in dire need of effective therapy, with the current standard of care options focusing on symptom management or offering limited clinical benefit. We believe BEN-34712 represents an exciting development in our research for a potential new treatment, particularly as it shows effectiveness in both the SOD1G93A mouse model system as well as familial and C9orf72 related ALS patient-derived cell models." About BenevolentAI BenevolentAI is a leading developer of advanced artificial intelligence technologies that unlock the value of multimodal data, surface novel insights, and accelerate biomedical discovery. Through the combined capabilities of its AI platform, its scientific expertise, and wet-lab facilities, the Company is developing an in-house drug pipeline of high-value assets. The Company is headquartered in London, with a research facility in Cambridge (UK) and a further office in New York. About ALS ALS is a progressive neurologic disorder characterised by the loss of cortical and spinal motor neurons, leading to the denervation of nerve endplates, axonal retraction and subsequent muscle atrophy. The average survival time following the initial diagnosis is around two-three years, and while there are drugs approved by the US FDA for ALS, they provide only modest benefits to patients, underwriting the urgent need for new and alternative therapies. About SITraN at the University of Sheffield The Sheffield Institute for Translational Neuroscience (SITraN) is an essential development in the fight against motor neurone disease and other common neurodegenerative disorders, including Parkinson's and dementia, as well as stroke and multiple sclerosis. SITraN has the potential to bring new treatments and new hope to patients and carers in the UK and worldwide, by significantly accelerating the pace of therapeutic development using technologies such as experimental modelling of disease, gene therapy and stem cell biology, gene expression profiling and bioinformatics analysis and modelling of the biological processes. Since its opening by Queen Elizabeth II in 2010, SITraN has grown immensely and developed into a leading global facility which is at the forefront of research and expertise.

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Twist Bioscience Launches Portfolio of RNA Sequencing Tools

Businesswire | May 23, 2023

Twist Bioscience Corporation a company enabling customers to succeed through its offering of high-quality synthetic DNA using its silicon platform, today announced the launch of a portfolio of RNA sequencing tools, which includes the Twist RNA Exome, Twist RNA Library Prep Kit and the Twist Ribosomal RNA (rRNA) & Hemoglobin (Globin) Depletion Kit, as well as custom target enrichment capabilities for RNA and whole transcriptome sequencing. This comprehensive suite of RNA tools can enable targeted or whole transcriptome research across fields including precision medicine, biomarker discovery and immuno-oncology research. “Twist’s RNA sequencing portfolio builds on our established NGS capabilities in genomic sequencing and methylation detection and expands into gene expression analysis, opening a new and significant market for Twist,” said Emily M. Leproust, Ph.D., CEO and co-founder of Twist Bioscience. “This offering allows our customers to leverage Twist’s leading target enrichment platform to discover and resolve low abundance RNA transcripts in the human transcriptome. Our RNA sequencing workflows are designed specifically for challenging samples. By enriching relevant transcripts, we can enable researchers to get high-quality data from a range of sample types, including damaged RNA.” Unlike the genome, which is relatively static, the transcriptome changes over time in response to varying disease states and drug therapies. Gene expression levels also differ across tissues and cell types. To fully understand this dynamic quality of RNA, researchers often sequence RNA samples from the same source at multiple time points, incurring additional costs and resource burdens. Each component of the Twist RNA sequencing portfolio is purpose-built to maximize data quality, minimize workflow inefficiency, decrease wasted sequencing reads, and support comprehensive transcriptomic profiling across even low-quality and low-input samples common in oncology. The Twist RNA sequencing portfolio provides end-to-end workflows that can be used to study total RNA and measure the whole transcriptome, protein coding sequences of messenger RNA (mRNA) or custom targets. These products can also be integrated into customers’ existing workflows. Twist RNA sequencing tools enable minimal hands-on time and increase the scale of samples sequenced through utilizing automation. They are compatible with a wide range of sample inputs, including difficult or low-quality samples. RNA panel designs can also now incorporate Twist’s new exon-aware design algorithm, which reduces bias in detection and can provide an important tool for researchers studying rare gene transcripts that drive tumor biology. Twist Targeted RNA Sequencing Workflow Twist target enrichment for RNA leverages the performance, efficiency and sensitivity of Twist target enrichment for sequencing of RNA transcripts of interest across samples and species. It can be used to enrich relevant transcripts with the RNA Exome or in custom RNA panels. Twist RNA Exome The Twist RNA Exome with Twist’s exon-aware design algorithm enables targeted sequencing of the protein coding regions of the human transcriptome without bias toward specific combinations of exons. The Twist RNA Exome covers up to 99.9% of protein coding sequencing in Gencode and RefSeq databases. This coverage, along with the exon-aware design approach, could enable researchers to capture important transcripts including those in low input and degraded samples from formalin fixed paraffin embedded (FFPE) sections. Twist Whole Transcriptome Sequencing Workflow Twist Whole Transcriptome Sequencing can be used to discover novel transcripts, including low expressing genes and novel isoforms. It can be used with a variety of samples including whole blood, fresh and frozen tissue samples and low quality samples, such as FFPE samples. The Twist rRNA & Globin Depletion Kit can be used with this workflow to deplete rRNA and hemoglobin targets so that researchers can study the rest of the transcriptome. The full workflow can be completed in less than five hours with minimal hands-on time. About Twist Bioscience Corporation Twist Bioscience is a leading and rapidly growing synthetic biology and genomics company that has developed a disruptive DNA synthesis platform to industrialize the engineering of biology. The core of the platform is a proprietary technology that pioneers a new method of manufacturing synthetic DNA by “writing” DNA on a silicon chip. Twist is leveraging its unique technology to manufacture a broad range of synthetic DNA-based products, including synthetic genes, tools for next-generation sequencing (NGS) preparation, and antibody libraries for drug discovery and development. Twist is also pursuing longer-term opportunities in digital data storage in DNA and biologics drug discovery. Twist makes products for use across many industries including healthcare, industrial chemicals, agriculture and academic research.

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Cellectis Presents Clinical Data on AMELI-01 and Preclinical Data on Multiplex Engineering for Superior Generation of CAR T-cells at ASGCT 2023

Globenewswire | May 18, 2023

Cellectis a clinical-stage biotechnology company using its pioneering gene-editing platform to develop life-saving cell and gene therapies, today presents clinical data on its Phase 1 AMELI-01 clinical trial (evaluating UCART123) that were unveiled in an oral presentation at the 64th American Society of Hematology (ASH) annual meeting, as well as preclinical data on multiplex engineering for superior generation of CAR T-cells, at the American Society of Gene and Cell Therapy (ASGCT) 2023 Annual Meeting. Preliminary Clinical Data from the AMELI-01 Study Presented at ASH 2022 AMELI-01 is a Phase 1 open-label dose-escalation trial evaluating the safety, tolerability, expansion and preliminary activity of UCART123 given at escalating dose levels after lymphodepletion (LD) with either fludarabine and cyclophosphamide (FC) or FC with alemtuzumab (FCA) in patients with relapsed or refractory acute myeloid leukemia (r/r AML). The oral presentation reviewed preliminary data from patients who received UCART123 at one of the following dose levels: dose level 1 (DL1) 2.5x105 cells/kg; dose level 2 (DL2) 6.25x105 cells/kg; intermediate dose level 2 (DL2i) 1.5x106 cells/kg; or dose level 3 (DL3) 3.30x106 cells/kg after lymphodepletion with FC ([n=8], DL1 – DL3) or FCA ([n=9], DL2 & DL2i). Preliminary Safety Data The FCA LD regimen resulted in robust lymphodepletion for greater than 28 days in all patients. Seven out of nine patients demonstrated UCART123 expansion, with maximum concentration (Cmax) ranging from 13,177 to 330,530 copies/μg DNA, an almost nine-fold increase compared with FC LD, and a significant increase in area under the curve (AUC) (0-28 days) (p=0.04; FC 10.2 vs. FCA 34.9). Cytokine release syndrome (CRS) occurred in eight patients in the FC arm and nine patients in the FCA arm. In the FC arm, one patient experienced Grade 3 immune effector cell-associated neurotoxicity syndrome (ICANS) and two patients experienced Grade 4 protocol-defined dose limiting toxicities (DLTs) secondary to CRS. In the FCA arm, two patients experienced Grade 5 DLTs secondary to CRS. Patient Enrollment in a 2-Dose Regimen Arm Overall, these preliminary data support the continued administration of UCART123 after FCA lymphodepletion in patients with r/r AML. Based on observed UCART123 expansion patterns and cytokine profiles, pursuant to an amended protocol, a second dose of UCART123 is given after 10-14 days to allow for additional UCART123 expansion and clinical activity without the use of additional lymphodepletion. The UCART123 cell expansion from the second dose of UCART123, in the setting of reduced disease burden, is expected to be safe and allow for clearance of residual disease. About Cellectis Cellectis is a clinical-stage biotechnology company using its pioneering gene-editing platform to develop life-saving cell and gene therapies. Cellectis utilizes an allogeneic approach for CAR-T immunotherapies in oncology, pioneering the concept of off-the-shelf and ready-to-use gene-edited CAR T-cells to treat cancer patients, and a platform to make therapeutic gene editing in hemopoietic stem cells for various diseases. As a clinical-stage biopharmaceutical company with over 23 years of experience and expertise in gene editing, Cellectis is developing life-changing product candidates utilizing TALEN®, its gene editing technology, and PulseAgile, its pioneering electroporation system to harness the power of the immune system in order to treat diseases with unmet medical needs. Cellectis’ headquarters are in Paris, France, with locations in New York, New York and Raleigh, North Carolina. Cellectis is listed on the Nasdaq Global Market and on Euronext Growth .

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CELL AND GENE THERAPY, AI

BenevolentAI Progresses BEN-34712 for the Potential Treatment of ALS into IND-Enabling Studies

Businesswire | June 05, 2023

BenevolentAI, a leader in the development of cutting-edge AI that accelerates biopharma discovery, announces the successful delivery of its pre-clinical candidate for the potential treatment of amyotrophic lateral sclerosis (ALS), BEN-34712. BEN-34712 is an oral, potent and selective brain penetrant RARɑβ (retinoic acid receptor alpha beta) biased agonist and will now enter investigational new drug (IND)-enabling studies. Impaired retinoic acid signalling has been shown to result in neuroinflammation, oxidative stress and mitochondrial dysfunction, all hallmarks of ALS. In preclinical studies conducted by the Company, BEN-34712 was neuroprotective in a patient-derived, disease-relevant in vitro motor neuron/iAstrocyte co-culture model, demonstrating significant efficacy in both sporadic and familial subtypes of ALS. In addition, BEN-34712 has demonstrated both central nervous system (CNS) target engagement and functional protective effects in the SOD1G93A mouse model of ALS after 50-day repeat dosing. BenevolentAI collaborated with the Sheffield Institute for Translational Neuroscience (SITraN) at the University of Sheffield on this programme, utilising their patient-derived motor neuron/iAstrocyte co-culture systems and in vivo model expertise. Anne Phelan, Chief Scientific Officer, BenevolentAI, said: “There remains a significant and urgent need for new and alternative therapies for patients with ALS. We are pleased by the promising advancement of our drug candidate, BEN-34712, towards clinical development, backed by the compelling preclinical data generated by our collaborators at SITraN.” Richard Mead, Senior Lecturer in Translational Neuroscience at SITraN, commented: "ALS patients suffering from this devastating neurodegenerative disease are in dire need of effective therapy, with the current standard of care options focusing on symptom management or offering limited clinical benefit. We believe BEN-34712 represents an exciting development in our research for a potential new treatment, particularly as it shows effectiveness in both the SOD1G93A mouse model system as well as familial and C9orf72 related ALS patient-derived cell models." About BenevolentAI BenevolentAI is a leading developer of advanced artificial intelligence technologies that unlock the value of multimodal data, surface novel insights, and accelerate biomedical discovery. Through the combined capabilities of its AI platform, its scientific expertise, and wet-lab facilities, the Company is developing an in-house drug pipeline of high-value assets. The Company is headquartered in London, with a research facility in Cambridge (UK) and a further office in New York. About ALS ALS is a progressive neurologic disorder characterised by the loss of cortical and spinal motor neurons, leading to the denervation of nerve endplates, axonal retraction and subsequent muscle atrophy. The average survival time following the initial diagnosis is around two-three years, and while there are drugs approved by the US FDA for ALS, they provide only modest benefits to patients, underwriting the urgent need for new and alternative therapies. About SITraN at the University of Sheffield The Sheffield Institute for Translational Neuroscience (SITraN) is an essential development in the fight against motor neurone disease and other common neurodegenerative disorders, including Parkinson's and dementia, as well as stroke and multiple sclerosis. SITraN has the potential to bring new treatments and new hope to patients and carers in the UK and worldwide, by significantly accelerating the pace of therapeutic development using technologies such as experimental modelling of disease, gene therapy and stem cell biology, gene expression profiling and bioinformatics analysis and modelling of the biological processes. Since its opening by Queen Elizabeth II in 2010, SITraN has grown immensely and developed into a leading global facility which is at the forefront of research and expertise.

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