Alternative splicing

Envisagenics Validates AI/ML Approach for RNA Target Identification and SSO Therapeutic Development

Retrieved on: 
Thursday, April 25, 2024
Cancer, Molecular Systems Biology, SSO, Machine learning, RNA, Artificial intelligence, Alternative splicing, Transforming growth factor beta, Entrepreneurship, Glomus tumor, Disease, Therapy, Patient, Metastasis, Validation, NEDD4L, Triple-negative breast cancer, TNBC

NEW YORK, April 25, 2024 /PRNewswire/ -- Envisagenics, an AI-driven biotechnology company, today announced the publication in the journal Molecular Systems Biology of study results evaluating the company's SpliceCore AI/ML platform in Triple Negative Breast Cancer (TNBC). This study demonstrates the efficacy of artificial intelligence and machine learning (AI/ML) for target discovery in triple negative breast cancer (TNBC) and for identifying functional and verifiable splice-switching oligonucleotides (SSOs) crucial for the development of RNA therapeutics. The results also validate its potential to tackle a challenging disease such as TNBC, a particularly aggressive cancer affecting approximately 200,000 patients annually, with a dismal five-year survival rate of only 20%. Detailed results from the study, titled "Development and Validation of AI/ML Derived Splice-Switching Oligonucleotides," are available here.

Key Points: 
  • While holding immense promise as a therapeutic approach for impeding cancer growth, the identification of functional SSOs using traditional methods is high cost and requires extensive time and labor.
  • "This study bridges the gap between computational predictions and experimental validation, positioning AI/ML as a critical force in validating RNA targets and advancing SSO therapeutic development," said Martin Akerman, Ph.D., Envisagenics' CTO and Co-Founder.
  • Validated a previously unidentified target in triple negative breast cancer (TNBC), NEDD4L exon 13 (NEDD4Le13), discovered through the SpliceCore platform.
  • "Our findings affirm the robustness and reliability of the platform and shed light on previously unrecognized avenues for therapeutic intervention."

Exonate first-in-class eye drop Phase Ib/IIa trial data demonstrate safety and biological activity in treatment of diabetic retinopathy and diabetic macular oedema

Retrieved on: 
Tuesday, March 5, 2024
Health, Diabetes, Clinical Trials, Research, Science, Optical, Biotechnology, Therapy, ARVO, Growth, Eye, Diabetic retinopathy, Safety, Alternative splicing, VEGF, Patient, Retinopathy, Phase, Trial of the century

These data demonstrate the safety and tolerability of EXN407, as well as clear indications of biological activity, positioning it well for further development as the first topical treatment for retinal vascular diseases such as diabetic retinopathy and diabetic macular oedema.

Key Points: 
  • These data demonstrate the safety and tolerability of EXN407, as well as clear indications of biological activity, positioning it well for further development as the first topical treatment for retinal vascular diseases such as diabetic retinopathy and diabetic macular oedema.
  • Exonate is now planning to progress EXN407 to the CLEAR-DM (Clinical Evaluation of a New Eyedrop for Alleviating Retinopathy in Diabetic Macular Oedema) Phase IIb clinical trial.
  • The mild NPDR/DME (NCT04565756) clinical study assessed the safety, tolerability and signals of biological response to EXN407 monotherapy in a double-masked, placebo-controlled Phase Ib/IIa dose-ranging clinical trial in treatment-naïve patients with mild/moderate non-proliferative diabetic retinopathy (NPDR) and mild diabetic macular oedema.
  • “The results suggest that topical ocular EXN407 may provide clinical benefit and substantially reduce the injection burden for patients with diabetic eye disease.

Singleron launches the AccuraSCOPE® Single Cell Transcriptome

Retrieved on: 
Tuesday, January 30, 2024
RNA-Seq, DNA, RNA, Workflow, Chromosome, Transcriptome, Disease, FASTQ, Genome, Data analysis, Messenger, Alternative splicing, Medicine, Computer data storage

COLOGNE, Germany, Jan. 30, 2024 /PRNewswire/ -- Singleron Biotechnologies, a leader in single cell multi-omic solutions for precision medicine, announced two new commercial product launches : AccuraSCOPE® Single Cell Transcriptome and Genome Library Kit and the AccuraSCOPE® Single Cell Full-Length Transcriptome Library Kit.

Key Points: 
  • COLOGNE, Germany, Jan. 30, 2024 /PRNewswire/ -- Singleron Biotechnologies, a leader in single cell multi-omic solutions for precision medicine, announced two new commercial product launches : AccuraSCOPE® Single Cell Transcriptome and Genome Library Kit and the AccuraSCOPE® Single Cell Full-Length Transcriptome Library Kit.
  • AccuraSCOPE  Single Cell Transcriptome and Genome Library Kit opens new possibilities for single cell multi-omic analysis by profiling the entire genome and transcriptome simultaneously.
  • In addition to single cell RNA sequencing, this method enables deep single cell genome sequencing, amplifying ultra-low quantities of DNA from individual cells.
  • It enables the detection of alternative splicing at the single cell level, substantially reducing hands-on time compared to existing full-length single cell RNAseq methods.

Gene Splicing Reduces Effectiveness of CD20-Targeting Monoclonal Antibodies Designed to Treat Variety of Blood Cancers and Disorders

Retrieved on: 
Friday, November 17, 2023
DOI, DRS, Malignancy, CHOP, Research, University, Bone marrow, Leukemia, Blood, Hospital, Protein, Jim Valvano, Patient, Lymphoma, Division, Follicular lymphoma, Messenger, Child, Medical laboratory, Virus, Burkitt lymphoma, Antibody, Exon, Children's Hospital of Philadelphia, Doctor of Philosophy, Emerson Collective, MS4A1, Alternative splicing, Bangladesh Technical Education Board, Cell, RNA, Vaccine, Pathology, CD20

PHILADELPHIA, Nov. 17, 2023 /PRNewswire/ -- Immunotherapies that target the CD20 antigen have revolutionized how patients with a variety of blood cancers and hematologic disorders have been treated. However, many patients develop resistance to these treatments due to a loss of the antigen that's being targeted. Now, a new study from researchers at Children's Hospital of Philadelphia (CHOP) and the Perelman School of Medicine at the University of Pennsylvania (Penn) has found that gene splicing occurring within these cells can cause significant changes in CD20 protein levels that render the therapies ineffective.

Key Points: 
  • PHILADELPHIA, Nov. 17, 2023 /PRNewswire/ -- Immunotherapies that target the CD20 antigen have revolutionized how patients with a variety of blood cancers and hematologic disorders have been treated.
  • These findings may lead to more appropriate choices for therapy that maximize benefits to patients affected by a variety of blood cancers.
  • CD20 is a cell-surface protein involved in the fine-tuning of B cell responses to foreign agents like viruses.
  • Prior research had shown that a loss of CD20 reduced the effectiveness of these immunotherapies, since it would remove their intended target.

Ultima Genomics to Present at ASHG and Provide Updated Reference Data Set

Retrieved on: 
Tuesday, October 31, 2023
Health, Genetics, Health Technology, Research, Science, Biotechnology, ASHG, Whole genome sequencing, Genomics, Stanford University, Booth, Genetic disorder, Alternative splicing, Centre for Industry Education Collaboration, UG, Society, Baylor College of Medicine, Fusion, ATAC, American Society of Human Genetics, Human genetics, Baylor, Scale, Ultima, Chemistry, Gene expression, Baylor University, Antibiotics, Music, Fine chemical, Communications satellite

Watchmaker Genomics will demonstrate gene fusion detection via cost-effective whole transcriptome sequencing using the optimized Watchmaker RNA Library prep kit.

Key Points: 
  • Watchmaker Genomics will demonstrate gene fusion detection via cost-effective whole transcriptome sequencing using the optimized Watchmaker RNA Library prep kit.
  • In conjunction with the conference, Ultima will be releasing a new data set demonstrating significant improvements to the technology made through early access.
  • In particular, the data demonstrates significant improvements in indel accuracy made through a variety of advancements across chemistry and bioinformatics.
  • Industry Education Session: Empowering Genomics at Scale Thursday, Nov. 2 | Room 140AB | Talks 3:30 - 4:30 p.m.

CHOP Researchers Develop Versatile and Low-Cost Technology for Targeted Long-read RNA Sequencing

Retrieved on: 
Tuesday, August 15, 2023
DNA, Medical laboratory, CHOP, Neoplasm, Biotin, Raymond, Nature Communications, Cancer, TEQUILA, RNA, Research, Child, Quantification, Genetic distance, Doctor of Philosophy, National Institutes of Health, Bangladesh Technical Education Board, Assistant, Alternative splicing, Protein, Dicarboxylic acid, Computation, Patent, Pathology, DOI, Hospital, Therapy, Gene, Science Publishing Group, Oligonucleotide, Breast cancer, Disease, Children's Hospital of Philadelphia, Fine chemical, Vaccine, Medical imaging

PHILADELPHIA, Aug. 15, 2023 /PRNewswire/ -- In a development that could accelerate the discovery of new diagnostics and treatments, researchers at Children's Hospital of Philadelphia (CHOP) have developed a versatile and low-cost technology for targeted sequencing of full-length RNA molecules. The technology, called TEQUILA-seq, is highly cost-effective compared to commercially available solutions for targeted RNA sequencing and can be adapted for different research and clinical purposes. The details were described in a paper in Nature Communications.

Key Points: 
  • The technology, called TEQUILA-seq, is highly cost-effective compared to commercially available solutions for targeted RNA sequencing and can be adapted for different research and clinical purposes.
  • "Targeted long-read RNA sequencing is a powerful strategy for elucidating the RNA repertoire for any predefined set of genes.
  • They are compatible for both targeted RNA and DNA sequencing, on both long-read and short-read sequencing platforms.
  • "TEQUILA-seq: A versatile and low-cost method for targeted long-read RNA sequencing," Nature Communications, August 8, 2023, DOI: 10.1038/s41467-023-40083-6

Seer Launches the Proteograph XT Assay Kit: Allowing Labs to Easily Expand Their View of the Proteome and Scale Their Studies

Retrieved on: 
Thursday, June 1, 2023
Data management, Organic and Biomolecular Chemistry, Nanoparticle, University, Therapy, Workflow, Cancer, Proteome, Research, Mass spectrometry, Proteomics, MS, Alternative splicing, Plasma, HIV disease progression rates, XT, Collection, University of Wisconsin–Madison, Biology, SEER, Fine chemical

Scope: Broadens the possibilities of novel proteomic studies by enabling access to a diverse set of species and sample types.

Key Points: 
  • Scope: Broadens the possibilities of novel proteomic studies by enabling access to a diverse set of species and sample types.
  • Scale: Enables large-scale studies powered for discovery, with data management tools that scale with it.
  • Seer’s Proteograph Product Suite with the Proteograph XT Assay Kit enables proteomics studies with an unprecedented combination of sight, scope, speed and scale, allowing an unbiased interrogation of the proteome to allow studies not previously possible.
  • The Proteograph Product Suite with the Proteograph XT Assay Kit makes it easy to add unbiased, deep, rapid proteomics studies at scale to any lab.

New Computational Tool Identifies Novel Targets for Cancer Immunotherapy

Retrieved on: 
Wednesday, May 17, 2023
Antigen, National academy, University, CHOP, IRIS, HLA, Nucleotide, National Cancer Institute, Eli, Survival, Cancer, Research, Child, RNA, Doctor of Philosophy, National Institutes of Health, Cancer Breakthroughs 2020, Proteomics, TCR, Alternative splicing, Genetic distance, Bangladesh Technical Education Board, Regenerative medicine, Stem cell, Cancer Research Institute, Protein, Molecular genetics, Hematological Cancer Research Investment and Education Act, Computation, Patient, Immune system, Peptide, DOI, Growth, Neoplasm, Hospital, UCLA, Protein isoform, RNA splicing, Disease, Children's Hospital of Philadelphia, Vaccine, Microbiology, NEPC, Immunotherapy, MD, Science, Immunology

PHILADELPHIA, May 17, 2023 /PRNewswire/ -- Researchers at Children's Hospital of Philadelphia (CHOP) and the University of California, Los Angeles (UCLA) have developed a computational platform capable of discovering tumor antigens derived from alternative RNA splicing, expanding the pool of cancer immunotherapy targets. The tool, called "Isoform peptides from RNA splicing for Immunotherapy target Screening" (IRIS), was described in a paper published today in the Proceedings of the National Academy of Sciences.

Key Points: 
  • "We know that aberrant alternative RNA splicing is widespread in cancer and generates a range of potential immunotherapy targets.
  • In our study, we were able to show that our computational platform was able to identify immunotherapy targets that arise from alternative splicing, introducing a broadly applicable framework for discovering novel cancer immunotherapy targets that arise from this process."
  • "This proof-of-concept study demonstrates that alternatively spliced RNA transcripts are viable targets for cancer immunotherapy and provides a big data and multiomics-powered computational platform for finding these targets," Dr. Xing added.
  • "IRIS: discovery of cancer immunotherapy targets arising from pre-mRNA alternative splicing," Proceedings of the National Academy of Sciences, online May 16, 2023, DOI: 10.1073/pnas.2221116120

Seer’s Proteograph™ Product Suite identifies undiscovered links between protein variants and lung cancer progression

Retrieved on: 
Wednesday, March 29, 2023
Nanoparticle, Complement component 1r, Bone morphogenetic protein 1, Senior, Complement component 4, Liquid biopsy, Cancer, Proteome, Research, Biomarker, Genomics, Lung cancer, Proteomics, Alternative splicing, Plasma, Protein, Patient, Division, Memorial Sloan Kettering Cancer Center, Biology, SEER, PLOS, Collagen, BMP1, Health, Tumor microenvironment, Disease, Messenger, Vaccine, NSCLC

from Memorial Sloan Kettering Cancer Center found previously unknown associations between four protein isoforms and non-small cell lung cancer (NSCLC) progression, constituting potential novel, disease-relevant biomarkers, or therapeutic targets.

Key Points: 
  • from Memorial Sloan Kettering Cancer Center found previously unknown associations between four protein isoforms and non-small cell lung cancer (NSCLC) progression, constituting potential novel, disease-relevant biomarkers, or therapeutic targets.
  • Importantly, the identified NSCLC-associated protein isoforms comprise structural variants of proteins that arise from distinct but related mRNAs produced from the same gene through the process of alternative splicing.
  • Notably, discovery and quantification of such protein variants in a complex biological sample requires deep, unbiased interrogation of the proteome at peptide-level resolution.
  • The Proteograph Product Suite makes it easy to add unbiased, deep, rapid proteomics studies at scale to any lab.

CHOP Researchers Develop New, More Accurate Computational Tool for Long-Read RNA Sequencing

Retrieved on: 
Friday, January 20, 2023
ESPRESSO, DSM-IV codes, Genetic distance, Gene, Computation, Alternative splicing, Children's Hospital of Philadelphia, Bangladesh Technical Education Board, DNA, National Institutes of Health, Computer, Cell, Science Advances, National Cancer Institute, CHOP, Promotion, Hospital, Protein, RNA, B cell, Cancer, Child, DOI, Computational genomics, Disease, Transcriptome, Doctor of Philosophy, Vaccine, Book

PHILADELPHIA, Jan. 20, 2023 /PRNewswire/ -- On the journey from gene to protein, a nascent RNA molecule can be cut and joined, or spliced, in different ways before being translated into a protein. This process, known as alternative splicing, allows a single gene to encode several different proteins. Alternative splicing occurs in many biological processes, like when stem cells mature into tissue-specific cells. In the context of disease, however, alternative splicing can be dysregulated. Therefore, it is important to examine the transcriptome – that is, all the RNA molecules that might stem from genes – to understand the root cause of a condition.

Key Points: 
  • ESPRESSO is a computational tool that addresses a long-standing problem of long-read RNA sequencing.
  • To circumvent this problem, researchers at Children's Hospital of Philadelphia (CHOP) have developed a new computational tool that can more accurately discover and quantify RNA molecules from these error-prone long-read RNA sequencing data.
  • The transition from short-read to long-read RNA sequencing represents an exciting technological transformation, and computational tools that reliably interpret long-read RNA sequencing data are urgently needed."
  • ESPRESSO can accurately discover and quantify different RNA molecules from the same gene – known as RNA isoforms – using error-prone long-read RNA sequencing data alone.