17 results about "RNA splicing" patented technology

The invention belongs to the field of biological medicine, and relates to a guide agRNA for regulating RNA splicing. The invention provides an application of a guide agRNA (Ribonucleic Acid) in preparation of a medicine for changing expression of a target protein by cells of a subject. The guide agRNA recruits ADAR protein to the 3 'splice site or pseudo 3' splice site to edit the A base of the 3 'splice site or pseudo 3' splice site, thereby splicing the whole exon located at the 3 'splice site or flanking the pseudo 3' splice site of the intron from the precursor mRNA, thereby changing the level of mRNA encoding the target protein, and altering the expression of the target protein in the cell. The target gene pre-mRNA selective splicing is regulated and controlled to influence the function or expression of the functional RNA and the target protein of the target gene, so that the purpose of treating diseases is achieved.

Systems and methods for identifying a diagnosis of a cancerous state for a somatic tumor specimen of a subject are provided.SOLUTION: The method receives sequencing information comprising an analysis of a plurality of nucleic acids from a somatic tumor specimen. The method identifies a plurality of features from the sequencing information including two or more of RNA, DNA, RNA splicing, viral, and copy number features. The method provides a first subset of features and a second subset of features from the identified plurality of features as input to a first classifier and a second classifier, respectively. The method generates two or more predictions of cancer status based at least in part on the identified plurality of features from the two or more classifiers. The method combines the two or more predictions with a final classifier to identify a diagnosis of cancer status for the subject's somatic tumor specimen.SELECTED DRAWING: Figure 1

Provided are heterocyclic compounds and related compositions that modulate nucleic acid splicing, as well as methods of use of the compounds for modulating splicing and treating diseases and conditions.

The invention discloses a method for identifying sheep testicular germ cells by an immunofluorescence technique based on DDX39A gene, and particularly relates to the technical field of animal breeding, which comprises the following steps: S1, embedding treatment; s2, antigen permeation; s3, antigen repair; s4, closing serum; s5, primary antibody incubation: DDX39A is diluted, and a primary antibody solution is prepared; s6, secondary antibody incubation: selecting a green fluorescence labeled antibody for dilution, and preparing a secondary antibody solution; s7, washing; s8, performing nucleus dyeing; s9, mounting and observing; and S10, analyzing the image. The DDX39A is adopted to replace existing VASA to mark germ cells in the testis, compared with the VASA, the DDX39A gene can participate in multiple processes such as RNA splicing, nuclear output, transcriptional regulation and DNA repair, and the DDX39A gene has the advantages of being diversified in function, suitable for multi-aspect research, high in flexibility and wide in sample source and has wide application prospects clinically.

The present invention relates generally to the field of RNA splicing. In particular, the invention relates to splice-switching oligonucleotides (SSOs) configured to alter the splicing of a IL-4Rα pre-mRNA. The invention also relates to a method of exon-skipping wherein the binding of the SSO to a IL-4Rα pre-mRNA induces the exclusion of an exon during splicing of the IL-4Rα pre-mRNA to a IL-4Rα mature mRNA. The invention also relates to the use of SSOs as therapeutic candidates for treating Th2-mediated inflammatory diseases.

The present application belongs to the field of biological medicine, and particularly relates to a non-small cell lung cancer shared neoantigen epitope peptide based on RNA splicing mutation, and an amino acid sequence of the neoantigen polypeptide is shown as SEQ ID No. 1-4. The present application has the following beneficial effects: 1. Improving the sharing: by focusing on the RNA abnormal splicing derived neoantigen, the present application aims to identify the neoantigen epitope peptide with high sharing and conservation, thereby providing a basis for developing a universal neoantigen vaccine. 2. Enhancing immunogenicity: the RNA variation derived neoantigen usually has stronger HLA binding capacity, and the present application can significantly improve the immunogenicity and therapeutic potential of the neoantigen by preferentially screening the RNA derived variation. 3. Population specificity optimization: combined with the HLA distribution characteristics of Chinese population, the present application is committed to developing a personalized neoantigen vaccine suitable for Chinese non-small cell lung cancer patients, and improving the accuracy and effectiveness of treatment.

The present invention relates generally to the field of RNA splicing. In particular, the invention relates to splice-switching oligonucleotides (SSOs) capable of altering the splicing of a pre-mRNA encoding a variant of the SLC25A13 gene. The invention also relates to the use of SSOs as therapeutic candidates for treating citrin deficiency. In an aspect of the invention, there is provided a method of exon-skipping comprising providing a splice-switching oligonucleotide (SSO) that binds to a site within a target region present on a pre-mRNA transcript of the SLC25A13 gene, wherein the binding of the SSO induces the exclusion of SLC25A13-PE5 from a mature mRNA transcript of the SLC25A13 gene. In another aspect, there is provided a splice-switching oligonucleotide (SSO) that binds to a site within a target region present on a pre-mRNA transcript of the SLC25A13 gene, the target region having at least 95% sequence identity to SEQ ID NO: 28, and wherein binding of the SSO induces the exclusion of SLC25A13-PE5 from a mature mRNA transcript of the SLC25A13 gene.

The invention relates to the technical field of molecular biology and genetic diagnosis, and particularly discloses an RNA (Ribonucleic Acid) abnormal splicing verification method and a kit, the method comprises the following steps: extracting whole blood RNA and reversely transcribing the whole blood RNA into cDNA (Complementary Deoxyribose Nucleic Acid); the method comprises the following steps: by taking cDNA (complementary deoxyribonucleic acid) as a template, carrying out first-round PCR (polymerase chain reaction) amplification by using an outer primer pair as shown in SEQ ID NO.2 and SEQ ID NO.3, and covering No.17 to No.26 exons of the OTOF gene; carrying out electrophoresis preliminary judgment on an amplification product; after a product is recovered, carrying out a second round of nested PCR amplification by using an inner primer pair as shown in SEQ ID NO.5 and SEQ ID NO.6, and covering the 20th exon, the 20th exon, the 23rd exon and the 23rd exon; and finally, sequencing a second-round amplification product, and comparing a wild type sequence to determine an abnormal mode. The kit comprises the primer pair. The method is directly based on a blood sample, operation is easy and convenient, genome DNA pollution is avoided through the design of the cross-exon primer, and the influence of mutation on RNA splicing can be accurately and specifically revealed.

Described herein is a pharmaceutical composition comprising a small molecule splicing modulator compound that modulates splicing of mRNA, such as pre-mRNA, encoded by genes, and methods of use of the small molecule splicing modulator compounds for modulating splicing and treating diseases and conditions.

Provided herein are methods and compositions for modifying RNA splicing of a pre-mRNA molecule to produce a modified mRNA molecule. The methods can comprise delivering to a cell one or more vectors or proteins comprising: (i) a nucleic acid molecule encoding one or more PAM-less or nearly PAM-less Cas nickases and one or more cytosine or adenosine deaminases or one or more PAM-less or nearly PAM-less Cas proteins and one or more cytosine or adenosine deaminase proteins; and a nucleic acid molecule encoding one, two, or more single guide RNA (sgRNA) molecules targeting a splice acceptor site and / or a splice donor site of a DNA molecule encoding the pre-mRNA. One or more exons or one or more portions of an exon are excluded during RNA splicing, resulting in the production of the modified mRNA molecule.

The invention belongs to the field of biological medicine, and particularly relates to a non-small cell lung cancer shared neoantigen epitope peptide based on RNA shear mutation, and the amino acid sequence of the neoantigen peptide is shown as SEQ ID No.1-4. Compared with the prior art, the method has the following beneficial effects: 1, the shareability is improved: by focusing the new antigen derived from RNA abnormal cleavage, the invention aims to identify the new antigen epitope peptide with high shareability and conservative property, so that a basis is provided for developing a universal new antigen vaccine; 2, the immunogenicity is enhanced: the new antigen derived from RNA variation generally has stronger HLA (human leukocyte antigen) binding capacity, and the immunogenicity and the treatment potential of the new antigen can be obviously improved by preferentially screening variation of RNA sources; 3, population specificity optimization: in combination with the HLA distribution characteristics of Chinese population, the invention aims to develop personalized new antigen vaccines suitable for Chinese non-small cell lung cancer patients, and the accuracy and effectiveness of treatment are improved.

The application discloses a long-read RNA splicing consistency scoring and recognition method, comprising the following steps: (1) extracting candidate splicing reads from the SAM or BAM format alignment results of long-read RNA sequencing data; (2) analyzing the splicing site coordinates of the candidate splicing reads; (3) grouping the candidate splicing events; (4) calculating the splicing consistency score; (5) determining the candidate splicing events according to rules; and (6) machine learning enhanced determination. The application takes the spatial distribution characteristics of the splicing sites in multiple reads as the core, defines the splicing consistency score, and quantitatively represents the site stability of the candidate splicing events. On this basis, the read support, splicing sequence characteristics and machine learning enhanced determination module are further combined to realize the hierarchical recognition and probability evaluation of the candidate splicing events, so that the accuracy, robustness and discovery ability of potential new splicing events of the splicing site recognition in the long-read RNA sequencing data are improved.

The present invention relates generally to the field of RNA splicing. In particular, the invention relates to splice-switching oligonucleotides (SSOs) capable of altering the splicing of a pre-mRNA encoding a variant of the ornithine transcarbamylase (OTC) gene. The invention also relates to the use of SSOs as therapeutic candidates for treating a urea cycle disorder, particularly OTC deficiency. In an aspect of the invention, there is provided a SSO that specifically binds to a site within a target region present on a pre-mRNA transcript of a variant of the OTC gene, the target region comprising the sequence of SEQ ID NO: 31, wherein the pre-mRNA transcript comprises a c.540+265G>A mutation and binding of the SSO induces the exclusion of pseudoexon OCT-PE5 from a mature mRNA transcript of the variant of the OTC gene.

The disclosure provides artificial nucleic acid introns configured for selective splicing in cells with aberrant RNA splicing activity, e.g., neoplastic cells. The artificial intron can comprise an upstream flanking exon, an upstream intron, an alternatively spliced “cassette” exon, a downstream intron, and a downstream flanking exon. Also provided are constructs integrating the artificial introns with exons in a configuration that, when the artificial intron is spliced out by the aberrant RNA splicing factors, encode a functional protein. Also disclosed are methods that employ the disclosed platform of selective expression, including, targeted gene therapy methods (e.g., in cancers), diagnostics and imaging, and drug screening.

The invention discloses an RNA splicing verification method for predictive guidance design and a kit, and belongs to the technical field of molecular biology and genetic diagnosis. The method comprises the following steps: firstly, predicting an abnormal splicing mode possibly caused by specific gene mutation through a bioinformatics tool; then, on the basis of a prediction result, PCR primers are specifically designed, so that abnormal splicing products and normal splicing products can be effectively distinguished; and finally, carrying out experimental verification through RT-PCR and product sequencing. According to the method, the blindness of primer design in traditional verification is overcome, and the detection efficiency and accuracy of complex and tiny splicing abnormity are remarkably improved. The invention also provides a method for verifying the OTOF gene c.3409-11Agt, and a kit for verifying the OTOF gene c.3409- The invention discloses a special primer kit for G mutation.

The invention discloses a tumor neoantigen polypeptide as well as a generation method and application thereof. The amino acid sequence of the tumor neoantigen polypeptide is as shown in SEQ ID NO. 12-33. According to the invention, the RNA binding motif protein 39 (RNA Binding Motif Protein 39, RBM39) is knocked down in a targeted manner through CasRx driven by a bladder cancer specific promoter, and the RNA splicing process is effectively interfered, so that the tumor specific neoantigen is successfully induced to be generated in bladder cancer cells, the technical bottlenecks of high antigen heterogeneity, low generation efficiency and the like in the traditional tumor neoantigen therapy are overcome, and the tumor specific neoantigen is obtained. Efficient generation of the tumor neoantigen is realized, a new treatment strategy and a technical path are provided for immunotherapy of bladder cancer, and the tumor neoantigen has important clinical transformation prospect and application potential.