87 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.

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.

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.

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.

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.

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.

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

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.

The application discloses a cell proportion prediction method and device fusing prior biological knowledge, and the method comprises the following steps: inputting mixed RNA expression data of a to-be-detected tissue sample into a pre-trained double-flow deconvolution model, wherein the double-flow deconvolution model comprises a feature extraction module and a feature fusion prediction module, the feature extraction module comprises two parallel branches: a deep neural network and a knowledge-driven sparse neural network, and the data processing process comprises the following steps: inputting the mixed RNA expression data into the deep neural network to extract a data-driven hidden layer high-dimensional feature vector; inputting the mixed RNA expression data into the knowledge-driven sparse neural network to extract a knowledge feature vector conforming to biological rules by using a pre-constructed knowledge mask; and inputting the hidden layer high-dimensional feature vector and the knowledge feature vector into a full connection layer and a Softmax activation function after splicing in the feature fusion prediction module, so as to obtain a prediction result of the proportion of each type of cell in the to-be-detected tissue sample.

The application provides application of a compound of a general formula I or a pharmaceutically acceptable salt, a hydrate, a solvate, a prodrug, a tautomer, a stereoisomer thereof as a MALT1 inhibitor, the MALT1 tumor inhibitor can inhibit the expression of a MALT1 gene or inactivate the function of a MALT1 protein, the compound of the general formula can play the role of inhibiting the expression of the MALT1 gene or inactivating the function of the MALT1 protein by affecting the expression of a MALT1 protein death domain. The screened small molecule compound can inhibit the RNA expression of a marker in tumor cells and delay tumor progression in a tumor model mouse; in addition, when the small molecule compound is combined with an immune checkpoint inhibitor, the small molecule compound can synergize with the immune checkpoint inhibitor, and the curative effect is significantly enhanced.

It was revealed 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. On the basis of the obtained results, a disease caused by cellular senescence can be treated with a substance that suppresses hSATII RNA or a substance that increases CTCF expression. Whether the disease is caused by cellular senescence can be diagnosed by measuring the expression 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 disease caused by cellular senescence, a method for screening the therapeutic drug, and a method for acquiring data for detecting a disease caused by senescence.

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

Provided herein are vectors with engineered regulatory sequences for expression of non-coding RNAs (ncRNAs). Regulatory sequences of expression vectors include a Pol III promoter and a binding site for a Pol II - associated transcription factor. Also provided are compositions comprising provided vectors and methods of using the same, e.g., for expression of ncRNAs, e.g., for gene editing.

Presented herein are systems and methods for determining a likelihood of responsiveness of a subject suffering from cancer to an anti-cancer therapy. A computing system may construct, based on ribonucleic acid (RNA) sequence data, a network. In the network, each node may be associated with a RNA expression and each edge may identify a weight metric between RNA expression levels for a pair of nodes. The computing system may perform, for a plurality of iterations, a diffusion operation throughout the network. The computing system may determine a curvature metric for each iteration using the weight metric defined by each edge or node of the network. The computing system may select a critical iteration based on a difference of curvature metrics. The computing system may apply a plurality of features of the network to a model to generate a score indicating the likelihood of responsiveness of the subject to the anti-cancer therapy.

Provided are synthetic constructs for providing an enhancer or variant thereof as a promoter to drive RNA expression, as well as nucleic acids, vectors, and cells encoding or comprising said constructs. Associated methods and pharmaceutical compositions for use in therapy are also provided herein.

Multi-modal approaches to predict tumor immune infiltration are based on integrating gene expression data and imaging features in a neural network-based framework. This framework is configured to estimate percent composition, and thus immune infiltration score, of a patient tumor biopsy sample. Multi-modal approaches may also be used to predict cell composition beyond immune cells via integrated multi-layer neural network frameworks.