118 results about "Rna expression" patented technology

The invention provides a UTR (Untranslated Region) sequence for improving mRNA (Messenger Ribonucleic Acid) stability and translation efficiency and application of the UTR sequence, and particularly provides an mRNA molecule which comprises a coding region for coding polypeptide or protein and a fragment thereof, a 5 'UTR sequence positioned at the upstream of the coding region and / or a 3' UTR sequence positioned at the downstream of the coding region, the 5 'UTR sequence is a nucleotide sequence as shown in SEQ ID NO: 1, and the 3' UTR sequence is a nucleotide sequence as shown in SEQ ID NO: 2; and / or, the 5 'UTR sequence is a nucleotide sequence as shown in SEQ ID NO: 3, and the 3' UTR sequence is a nucleotide sequence as shown in SEQ ID NO: 4. According to the present invention, the mRNA stability and the translation efficiency are improved through the new and optimized UTR sequence, and the UTR sequence can be used as the element for enhancing the RNA expression efficiency in the nucleic acid treatment drug or the mRNA vaccine so as to provide more and better choices for the mRNA therapy.

Compositions and methods for assessing relative macromolecule abundance (for example, RNA expression levels) in a spatially-defined manner across a tissue sample (for example, from brain, lung, liver, kidney, pancreas, and / or heart) are disclosed, specifically providing deep transcriptomic coverage at high-resolution (for example, at approximate 10 μm (single cell) resolution) across multiple locations assessed across the tissue sample.

The invention discloses a conjugate of antisense oligonucleotide and polypeptide as well as a preparation method and application of the conjugate, belongs to the technical field of biological medicine, and provides the conjugate of antisense oligonucleotide and polypeptide, the structural general formula of the conjugate of antisense oligonucleotide and polypeptide is as shown in formula (I), O is antisense oligonucleotide, L is a connexon, and P is polypeptide; the antisense oligonucleotide is a nucleotide sequence obtained by modifying thiophosphate and 2 '-O-methyl on the basis of a nucleotide sequence as shown in SEQ ID NO.1 or a nucleotide sequence as shown in SEQ ID NO.2; and the amino acid sequence of the polypeptide is as shown in SEQ ID NO.3. According to the conjugate of the antisense oligonucleotide and the polypeptide, a phosphodiester bond of RNA is catalyzed by the polypeptide P to break, the antisense oligonucleotide O is complementarily paired with a frame-shift element, the polypeptide P is brought to the vicinity of the frame-shift element for targeted cleavage, and a linker L is responsible for coupling, sequence-specific targeted degradation of pathogenic RNA and destruction of the expression condition of RNA in cells.

Aspects of the invention provide an AAV product that delivers an STXBP1 gene supplementation or replacement strategy throughout the human CNS at levels of DNA biodistribution, RNA expression, and hSTXBPlb protein levels expected to restore function in STXBP1 encephalopathy patients.

Disclosed is a single cell analysis device for analyzing a tumor using artificial intelligence, the device including, a memory, and a processor, and the processor is configured to acquire single cell data on a tumor of a particular patient through the communication part; pre-process the single cell data on the tumor through a data pre-processing module; classify a type of the single cell based on the data pre-processed by a cell type defining module; predict a phenotype derivable from RNA expression of the tumor of the particular patient through a single-cell state predicting module materialize heterogeneity of the tumor of the particular patient through the tumor analyzing module; and report and provide an analysis result of the tumor of the particular patient through an analysis result generating module.

Antisense oligonucleotides and artificial expression constructs for modulating RNA expression in targeted central nervous system cell types are described. The artificial expression constructs can be used to express RNA in GABAergic neurons. Antisense oligonucleotides and artificial expression constructs can be used to rescue sodium voltage-gated channel function to treat disorders such as epilepsy, and more particularly, Dravet Syndrome, among many other uses.

Provided is a method for objectively evaluating the exercise habits and motor function of a subject in a simple and accurate manner. The present invention is characterized by comprising: a measurement step for measuring the RNA expression level of any one of Hif1, PHD3, GLUT1, GLUT3, and MCT4 in leukocytes in a peripheral blood sample of the subject; a cutoff value setting step for creating a receiver operating characteristic (ROC) curve and setting a predetermined cutoff value; and an evaluation step for statistically processing, by a chi-squared test, a boundary for evaluating the presence or absence of an exercise habit, and comparing the RNA expression level of the subject as measured in the measurement step and the cutoff value set in the cutoff value setting step, thereby evaluating the presence or absence of the exercise habit of the subject.

The present invention discloses a method for using a biotherapy for novel coronavirus (SARS-CoV-2) infection, wherein the protein is DEFA1 (human defensin α1, or human neutrophil peptide, HNP-1). The reagents include but are not limited to: 1) DEFA1 recombinant protein; 2) a vector containing a DEFA1 encoding gene; 3) a reagent for detecting RNA expression of DEFA1. The experimental research results of the present invention provide a new biotherapy method for novel coronavirus infection, and provide a new drug target for treating respiratory tract lesions caused by novel coronavirus infection.

It was discovered that by binding to CTCF which is important for maintaining chromosomal structures, hSATII RNA inhibits the function thereof, changes chromosome interaction, and induces transcription of inflammation-associated genes. It has also been discovered that cell death can be selectively induced in senescent cells and cancer cells by suppressing hSATII RNA expression. From the obtained results, it has been found that cancer treatment which targets senescent stromal cells and cancer cells can be performed with a substance that suppresses hSATII RNA or a substance that increases CTCF expression. In addition, cancer can be detected early by measuring the expression and activity of hSATII RNA and CTCF, and an epigenomic change of the hSATII DNA region. Thus, it is possible to provide a therapeutic drug for a cancer associated with cellular senescence, a method for screening thereof, and a test support method.

The present invention belongs to the field of gene expression data analysis, and particularly relates to a method for constructing a graph neural network data set based on gene expression; it includes obtaining gene expression profile data of a disease and extracting RNA data, processing the RNA data to generate an RNA expression matrix; performing standardization processing and differential analysis on the generated RNA expression matrix to obtain a differential expression matrix; using WGCNA to analyze the differential expression matrix and construct an overlapping topological matrix; exporting all edge information and node information in the overlapping topological matrix, and encoding the exported information; screening the encoded information, using the screened information to construct a graph neural network data set, and identifying biomarkers according to the graph neural network data set; the present invention performs WGCNA analysis on differentially expressed genes, pays attention to the relationship between genes, and constructs a graph neural network data set by screening node and edge information, which is beneficial to discovering biomarkers of tumors.

The present disclosure is directed to a split ribozyme biosensor system. Additionally, a genetically modified plant, plant tissue, or plant cell comprising the split ribozyme biosensor system is described. Methods for examining in vivo RNA expression in plants, plant cells or plant tissues are disclosed. Lastly, disclosed herein is a kit comprising the split ribozyme biosensor system.

Described herein are techniques for predicting whether a subject will respond to an immune checkpoint inhibitor (ICI) therapy based on RNA expression data and cytometry data obtained for the subject. In some embodiments, the techniques include: obtaining the RNA expression data, the RNA expression data having been previously obtained from a tumor sample from the subject; selecting, using the RNA expression data, an MF profile type for the tumor sample; obtaining the cytometry data, the cytometry data having been previously obtained from a blood sample from the subject; determining, using the cytometry data, a G2 score for the blood sample, wherein the G2 score is indicative a likelihood that the blood sample is of a Primed (G2) immunoprofile type of multiple immunoprofile types; and predicting, based on the selected MF profile type and the G2 score, whether the subject will respond to the ICI therapy.

The application belongs to the technical field of biological medicine, and particularly relates to application of long-chain non-coding RNA expression inhibition in esophageal cancer ferroptosis inducer sensitization. The application first reveals dynamic change of long-chain non-coding RNA ENSG00000250658 in esophageal squamous cell carcinoma metastasis based on single-cell sequencing data, detects expression of ENSG00000250658 in esophageal squamous cell carcinoma tissue and correlation with prognosis by using LNA probe-based RNA in-situ hybridization technology, and first finds that knocking down ENSG00000250658 can increase killing effect of ferroptosis inducer on esophageal squamous cell carcinoma cells. Therefore, the application provides a new technical scheme and thought for clinical diagnosis and treatment of esophageal cancer.

To provide systems and methods for performing quality control analysis.SOLUTION: This method obtains a batch dataset comprising, for each respective sample in a batch of samples, a corresponding plurality of sequence reads derived from the respective sample by targeted or whole transcriptome RNA sequencing, and corresponding metadata for the respective sample. The method determines for the batch dataset a cohort-matched reference batch, where the cohort-matched reference batch is balanced for tissue site, tumor purity, cancer type, sequencer identity, or date sequenced. The method performs global batch quality control tests on the batch dataset using at least the cohort-matched reference batch. The method removes respective samples from the batch dataset that fail any one of the one or more global batch quality control tests or flagging for manual inspection respective samples that fail any one of the one or more global batch quality control tests.SELECTED DRAWING: Figure 14

In certain examples, computer-implemented methods involve assessing patient diagnosis utilizing RNA expression profiles. As may be implemented in accordance with one or more aspects characterized herein, a landscape of RNA expression profiles may be generated from a plurality of patients having a set of common medical attributes. An RNA expression profile is obtained for a target patient having the medical attributes, and a plurality of nearest neighbor RNA expression profiles are identified from the landscape of RNA expression profiles, based on the target patient's RNA expression profile. A diagnosis for the target patient is provided based on known characteristics of the plurality of patients corresponding to the identified nearest neighbor RNA expression profiles.

The invention relates to the field of gene engineering, in particular to a cascade reaction-based plasmid elimination module, which comprises three types of mutually independent expression regions, one type of the expression regions is an antisense RNA expression region and comprises antisense RNA, a promoter of the antisense RNA and a terminator, and the other type of the expression regions is an antisense RNA expression region and comprises antisense RNA, a promoter of the antisense RNA and a terminator of the antisense RNA. The antisense RNA is the antisense RNA of a metabolic key gene mRNA, and can be combined with the metabolic key gene mRNA to hinder the translation of the metabolic key gene mRNA; the first region is an antisense neutralizing RNA expression region and comprises antisense neutralizing RNA, an inducible promoter of the antisense neutralizing RNA and a terminator of the antisense neutralizing RNA; the last type of region is a transcription factor region and is composed of constitutive promoters carried by a transcription factor fragment, and the constitutive promoters comprise an RNA polymerase binding site, a transcription start site, a ribosome binding site, a transcription factor translation region and a terminator; the antisense neutralizing RNA is an RNA fragment which is complementary with the antisense RNA in sequence, can be combined with the antisense RNA to enable the antisense RNA not to be combined with the metabolic key gene mRNA, and inhibits the antisense RNA from generating translation obstruction on the metabolic key gene mRNA. The method is high in elimination efficiency, elimination objects can be freely set according to needs, and selective or synchronous elimination of various plasmids can be realized.

The application discloses a kind of for sensitizing lung cancer radiotherapy biomimetic nano delivery system and preparation method and application, it belongs to the field of biological medicine, wherein, biomimetic nano delivery system is core-shell structure, including core and the shell of the core outer layer being wrapped;Wherein, core is the lipid nanoparticle of therapeutic nucleic acid being loaded;Shell is tumor cell membrane vesicle;Therapeutic nucleic acid is the short hairpin RNA expression plasmid of targeted deubiquitinating enzyme CYLD gene.The application solves lung cancer radiotherapy resistance problem from mechanism, by therapeutic nucleic acid specific knockdown deubiquitinating enzyme CYLD gene, effectively blocks CYLD / NRP1 signal shaft, to reverse the metabolic reprogramming of tumor cell, significantly enhance its radiotherapy sensitivity, realize to the low-toxicity treatment of radiation resistance lung cancer.

The invention discloses a sequence for improving the expression efficiency of circular RNA, a sequence combination and application of the sequence and the sequence combination, circular RNA expression plasmids are constructed through the sequence or the sequence combination, and the efficiency of expressing the circular RNA through the plasmids can be remarkably improved. The sequence, the sequence combination and the annular RNA expression plasmid disclosed by the invention can be used for preparing annular RNA drugs, and the expression efficiency of the target annular RNA is improved by delivering the drugs into cells, so that the sequence, the sequence combination and the annular RNA expression plasmid have important significance on treatment of diseases caused by low expression quantity of the annular RNA and research and development of corresponding drugs.

Aspects of the invention provide an AAV product that delivers an FXN gene supplementation or replacement strategy throughout the human CNS and heart at levels of DNA biodistribution, RNA expression, and FXN protein levels expected to restore function in Friedrich's ataxia patients.

The invention discloses a repair gene editing system aiming at HbE hematopoietic stem progenitor cell mutation site point mutation as well as a construction method and application thereof. The system comprises a nick RNA (Ribonucleic Acid) expression vector, an mRFP1 part, a peg expression vector plasmid and PEmax mRNA, wherein the nick RNA expression vector is formed by carrying out T4 connection on a vector skeleton obtained by carrying out enzyme digestion on pGL3-U6 plasmids and an oligo double-stranded DNA (Deoxyribose Nucleic Acid) sequence formed after annealing; the mRFP1 part is used for cutting off pU6-tevopreq1-GG-acceptor plasmids; the peg expression vector plasmid is used for inserting a redundant part into a designed peg-RNA sequence; the construction method comprises the following steps: firstly, determining a beta-thalassemia mutation site (beta CD26), then constructing a plasmid expression vector (a nick RNA expression vector is subjected to enzyme digestion, purification, connection design and other steps, and a peg expression vector is subjected to excision and sequence insertion), then transfecting a cell screening system by using lipo3000, determining the transfection efficiency, screening out sgRNA2 with high transfection rate, and using the sgRNA2 to prepare a kit. The method is used for accurately repairing Yunnan high-incidence beta-thalassemia mutation sites caused by point mutation of HbE hematopoietic stem / progenitor cell mutation sites.

This invention provides drugs and methods for the targeted delivery of payloads to cells. These drugs and methods are useful for delivering therapeutic or diagnostic agents to target cells. [Solution] In one embodiment, the present invention includes the step of administering RNA encoding a peptide or polypeptide (docketing compound) comprising a binding portion that binds to a target cell (primary targeting portion) and a further binding portion (secondary target) that binds to a drug comprising a payload (effector probe). After RNA expression, the primary targeting portion may bind to a target antigen such as a cancer antigen on a cancer cell, and then the secondary targeting portion contained in the effector probe may target the secondary target, thereby accurately delivering the "payload" to the target cell such as a cancer cell.

The invention discloses a sequence optimization method for improving the stability of circular RNA, application and a product, and belongs to the technical field of biotechnology and molecular biology. In order to solve the problem that the existing circular RNA is easy to be specifically degraded by RNAseK and lysosome after entering a cell, synonymous mutation optimization is carried out on an open reading frame of a target gene of the circular RNA by identifying nucleic acid motifs (a first type of nucleic acid motifs and a second type of nucleic acid motifs) identified by two degradation mechanisms. The optimized circular RNA is prepared by means of in-vitro cyclization of an anabaena I-type intron self-splicing mediator, after cells are transfected, the intracellular RNA expression level of the circular RNA is remarkably improved compared with that of a wild type, and the target protein expression efficiency is also remarkably improved. The intracellular stability and expression efficiency of the circular RNA are remarkably enhanced, and the method can be widely applied to the scenes of gene expression regulation, protein synthesis, gene therapy, vaccine development and the like.

Provided herein are methods, compositions, systems, kits and uses for integrated, simultaneous spatial multiomic analyses of tissues and samples including chromatin accessibility epigenomic analysis, RNA expression transcriptomic analysis, cell cluster and cell lineage analysis, transcription factor motif analysis, extrachromosomal DNA analysis and mitochondrial DNA analysis.

Systems and methods are provided for performing quality control analysis. The method obtains, in electronic form, a batch dataset comprising, for each respective sample in a batch of samples, a corresponding plurality of sequence reads derived from the respective sample by targeted or whole transcriptome RNA sequencing and corresponding metadata for the respective sample. The method determines for the batch dataset a cohort-matched reference batch, where the cohort-matched reference batch is balanced for tissue site, tumor purity, cancer type, sequencer identity, or date sequenced. The method performs one or more global batch quality control tests on the batch dataset using at least the cohort-matched reference batch. The method removes respective samples from the batch dataset that fail any one of the one or more global batch quality control tests or flagging for manual inspection respective samples that fail any one of the one or more global batch quality control tests.

The invention provides scalable methods for measuring chromatin accessibility and RNA expression in the same single cells by connecting chromatin accessibility and transcriptome.

The invention relates to the technical field of biology, in particular to a modeling method for rapidly preparing a humanized monkey model, which comprises the following steps: S1, constructing an AAV9-ACE2-GFP vector, observing the expression condition of GFP, and detecting the expression condition of ACE2 in infected cells in combination with flow cytometry; s2, directionally infecting the lung of the mouse with an AAV9-ACE2 virus, and detecting the RNA expression level of human ACE2 to verify the expression effect of the AAV9-ACE2 virus in the mouse body; s3, the AAV-ACE2 virus is targeted to the lung organ of the monkey, and the expression quantity of the human ACE2 gene in the lung tissue is detected through Q-PCR; and S4, carrying out a novel coronavirus infection experiment by using the humanized monkey model obtained in the step S3. The method comprises the following steps: firstly, establishing a virus delivery mode to carry out humanization on lungs of non-human primates; the genetically modified monkey is further subjected to a challenge experiment, a monkey model more susceptible to novel coronavirus is prepared, and a humanized monkey can be rapidly generated to be used for evaluating novel coronavirus related drugs.

The invention relates to the technical field of gene engineering, and discloses a molecular marking method and system for an RNA regulatory network of lncRNA UCA1 in cerebral ischemia injury, and the method comprises the following steps: establishing a cerebral ischemia injury scene of an experimental subject, and analyzing the interaction between the lncRNA UCA1 and other RNAs; the method comprises the following steps: performing scene grading on a cerebral ischemia injury scene, and measuring lncRNA UCA1, target RNA, a biological pathway of an experimental subject and lncRNA UCA1 expression related substances, target RNA expression related substances, biological pathway quantity and ischemia related cell data of ischemia related cells of the experimental subject in the graded scene; the cell numerical value of the ischemia related cell is calculated, and the lncRNA UCA1 expression level of the lncRNA UCA1 is analyzed by using the lncRNA UCA1 expression related substance; identifying cell-grading association and pathway-grading association between the cell numerical value and the grading scene and between the biological pathway quantity and the grading scene; the molecular marker in the cerebral ischemia injury scene is selected from the lncRNA UCA1 and the target RNA by using RNA-cell association and RNA-pathway association. According to the invention, the numeralization ability of the molecular marker in cerebral ischemia injury can be improved.

This invention provides UTR sequences for improving mRNA stability and translation efficiency, and their applications. Specifically, it provides an mRNA molecule comprising a coding region encoding a polypeptide or protein and its fragments, a 5′ UTR sequence upstream of the coding region, and / or a 3′ UTR sequence downstream of the coding region. The 5′ UTR sequence is the nucleotide sequence shown in SEQ ID NO:1, and the 3′ UTR sequence is the nucleotide sequence shown in SEQ ID NO:2; and / or, the 5′ UTR sequence is the nucleotide sequence shown in SEQ ID NO:3, and the 3′ UTR sequence is the nucleotide sequence shown in SEQ ID NO:4. This invention improves mRNA stability and translation efficiency through novel and optimized UTR sequences, which can be used as elements to enhance RNA expression efficiency in nucleic acid therapeutics or mRNA vaccines, providing more and better options for mRNA therapy.

The invention belongs to the technical field of biological genes, and discloses a method for identifying RNA interaction protein based on a Turbo ID technology and an MCP / MS2 system, the method can be used for identifying protein interacting with RNA in vitro or in vivo, and the method specifically comprises the following steps: firstly, respectively constructing RNA expression vectors inserted with MS2 tags, then constructing fusion protein vectors expressing MCP-Turbo ID, and finally constructing fusion protein vectors for expressing MCP-Turbo ID; the method comprises the following steps of: inserting RNA (Ribonucleic Acid) into an MS2 tag, transgenosis into a plant receptor by utilizing an agrobacterium tumefaciens mediated genetic transformation method to obtain a transgenic plant material expressing MCP-Turbo ID, combining the RNA inserted with the MS2 tag with the MCP-Turbo ID in vivo / in vitro by utilizing a hybridization or in-vitro incubation method, further enabling the Turbo ID to be adjacent to the RNA, biotinylating the RNA binding protein, and obtaining a transgenic plant material expressing the MCP-Turbo ID. And then enriching biotinylated protein by adopting streptavidin magnetic beads, and identifying and analyzing through Western Blot and mass spectrometry. The method not only solves the problem that the interaction protein of specific RNA in a living cell environment cannot be effectively identified in the prior art, but also can capture a transient or low-affinity RNA-protein interaction relationship.

The invention relates to the technical field of agriculture, in particular to an efficient ABE base editing tool based on Cas12i3 and application of the efficient ABE base editing tool. The Cas12i3-based efficient ABE base editing tool provided by the invention comprises a protein expression cassette and an RNA (Ribonucleic Acid) expression cassette, the protein expression cassette comprises a promoter, a 2 * BP NLS nuclear localization signal fragment, a 2 * adenine deaminase TadA8e, a connecting peptide, a Cas12i3 notch enzyme fragment and a terminator, the RNA expression cassette comprises a promoter, a crRNA sequence and a terminator; wherein the crRNA sequence is composed of a DR sequence and a target specific spacer sequence. The tool realizes efficient and specific single base substitution of A-to-G in a rice genome by utilizing the targeted binding characteristic of Cas12i3 and the efficient deamination activity of 2 * TadA8e, has the advantages of high editing efficiency, low off-target rate, wide application range and the like, provides an efficient and accurate technical means for plant functional genome research and molecular breeding, and has a wide application prospect. The creation of excellent rice varieties can be accelerated.