Precision-based immuno-molecular augmentation (PBIMA) computerized system, method, and therapeutic vaccine
Inventors
Khan, Shamsuddin Sultan • Catanzaro, John A. • Yuryev, Anton
Assignees
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Publication Number
US-11887710-B2
Publication Date
2024-01-30
Expiration Date
Abstract
As disclosed herein a precision based immunomolecular augmentation (PBIMA) high specificity patient profiling networked computer system, rapid therapeutic vaccine design method, and personalized vaccine, which utilizes immuno-molecular biopathway HLA affinity mapping and selection prediction ranking tools. This PBIMA approach comprises: Strategic-Selection, Molecular-Mapping, Antigen-Alignment, Receptor-Recognition, and Tactical Technology (SMART). The platform obtains data from a patient's genes and proteins as input. NGS data, including WES, WGS, ctDNA and cfDNA, RNAseq uses as input. PBIMA comprises a gene-protein-cell Cloud-based sequence editing interface to select the high confidence peptides. The PBIMA vaccine is a solution-based multi-purpose vaccine design strategy. PBIMA technology can produce therapeutic vaccines for cancer, autoimmune, neurodegenerative, inflammation-driven disease, and novel pathogen infection treatment. PBIMA therapeutic design is multi-mechanistic and broad-spectrum.
Core Innovation
The patent describes a precision-based immunomolecular augmentation (PBIMA) computerized, cloud-based method for designing and treating a patient with customized therapeutic peptides or a peptide vaccine. The method receives patient data comprising one or more of patient transcriptomics data and patient urine proteomics data, and computes a precision data output of a vaccine composition comprising a plurality of ranked peptide sequences encoding self-antigens and/or neo-antigens.
The ranked peptide sequences are computed to encode peptides for CD4+/CD8+ natural killer (NK) cell modulation specific to a patient's profile and able to elicit an effective therapeutic response against a patient disease. The PBIMA method further computes CRISPR prime editing and intracellular multi-core processing on the vaccine composition to produce a DNA-RNA and epigenetic modulation plurality of immunopeptide sequences.
In the system level disclosure, the patent describes a cloud-based computer system comprising a precision based immunomolecular augmentation computing platform with online databases and application programming interfaces (APIs). The platform includes next-generation sequencing (NGS) OMICS file processing, a Peptide Analysis Tool, a Susceptibility Tool, a Genome Uniqueness component, a Gene-Protein-Disease Interaction Database, and a Sequence Integrity module, and includes PBIMA Unification API (Neo7Logix Cloud base integrative API) to design and rank neoantigens of 9-aminoacid peptides-MHC-I and 12-aminoacid peptides-MHC-II.
Claims Coverage
The independent claims cover seven inventive features across a PBIMA computerized cloud-based method, a cloud-based PBIMA computing system, and a personalized peptide vaccine composition. The claims focus on patient transcriptomics and urine proteomics inputs, ranked self-antigen and neo-antigen peptide design for CD4+/CD8+ NK cell modulation, CRISPR prime editing with intracellular multi-core processing, immunopeptide synthesis/manufacturing, delivery for administration, and modular cloud platform components for ranking neoantigens.
Cloud-based PBIMA peptide vaccine design from transcriptomics and urine proteomics
Receiving patient transcriptomics data and patient urine proteomics data; computing a precision data output of a vaccine composition comprising a plurality of ranked peptide sequences encoding self-antigens and/or neo-antigens for CD4+/CD8+ natural killer (NK) cell modulation specific to a patient's profile.
CRISPR prime editing with intracellular multi-core processing to produce DNA-RNA and epigenetic modulation immunopeptide sequences
Computing a CRISPR prime editing and an intracellular multi-core processing on the vaccine composition to produce a DNA-RNA and epigenetic modulation plurality of immunopeptide sequences.
Immunopeptide synthesis and delivery for administration
Conducting an immunopeptide synthesis and manufacturing of the vaccine composition; and conducting the delivery of the vaccine composition to a patient's clinician or institution for administration to the patient.
Cloud-based PBIMA platform components and APIs for ranked neoantigen design
A precision based immunomolecular augmentation (PBIMA) computing platform comprising online databases and application program interfaces (APIs), including NGS OMICS file processing, a Peptide Analysis Tool, a Susceptibility Tool, a Genome Uniqueness component, a Gene-Protein-Disease Interaction Database, a Sequence Integrity module, PBIMA Unification API to design and rank neoantigens of 9-aminoacid peptides-MHC-I and 12-aminoacid peptides-MHC-II, and a Payload API.
Networked patient omics input transmission and therapeutic peptide selection
A plurality of local and/or remote computers transmit patient input data comprising NGS, WES, RNAseq, circulating DNA (ctDNA and cfDNA), and urine proteomics data to a PBIMA editing system; the personalized peptide vaccine comprises about 5 to about 20 peptide sequences computed to be the most therapeutically effective for treating the patient.
Personalized peptide vaccine composition encoding self-antigens and neo-antigens
A plurality of peptide sequences encoding self-antigens and neo-antigens for a CD4+/CD8+ natural killer (NK) cell modulation specific to a patient's profile, and able to elicit an effective therapeutic response against a patient disease.
Cloud-based computation and CRISPR prime editing to produce immunopeptide sequences
Receiving patient transcriptomics data and patient urine proteomics data; computing a precision data output of a vaccine composition comprising a plurality of therapeutic peptide sequences encoding peptides, self-antigens or neo-antigens specific to a patient's profile; and computing CRISPR prime editing and intracellular multi-core processing to produce a DNA-RNA and epigenetic modulation plurality of immunopeptide sequences.
The claims cover a PBIMA cloud-based workflow and system that uses patient transcriptomics and urine proteomics to compute ranked self-antigen and neo-antigen peptides for CD4+/CD8+ NK cell modulation, uses CRISPR prime editing with intracellular multi-core processing to produce DNA-RNA and epigenetic modulation immunopeptide sequences, and includes immunopeptide synthesis, manufacturing, and delivery for administration.
Stated Advantages
Documented Applications
Treating and/or designing a customized therapeutic peptides or peptide vaccine for a patient having one or more diseases comprising a cancer, an autoimmune disease, a neurodegenerative disease, and/or a pathogenic infectious disease.
Designing and administering a personalized peptide vaccine computed to be most therapeutically effective by eliciting CD4+/CD8+ NK cell modulation specific to a patient's profile.
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