1,620,236 results match your criteria gene expression

Type III-A CRISPR-Cas systems as a versatile gene knockdown technology.

RNA 2022 May 26. Epub 2022 May 26.

University of Georgia;

CRISPR-Cas systems are functionally diverse prokaryotic anti-viral defense systems, which encompass six distinct types (I-VI) that each encode different effector Cas nucleases with distinct nucleic acid cleavage specificities. By harnessing the unique attributes of the various CRISPR-Cas systems, a range of innovative CRISPR-based DNA and RNA targeting tools and technologies have been developed. Here, we exploit the ability of type III-A CRISPR-Cas systems to carry out RNA-guided and sequence-specific target RNA cleavage for establishment of research tools for post-transcriptional control of gene expression. Read More

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Multiple genomes reveal distinct evolutionary dynamics between de novo candidates and duplicated genes.

Genome Res 2022 May 26. Epub 2022 May 26.

Max Planck Institute for Biology

The birth of new genes is a major molecular innovation driving phenotypic diversity across all domains of life. Although repurposing of existing protein-coding material by duplication is considered the main process of new gene formation, recent studies have discovered thousands of transcriptionally active sequences as a rich source of new genes. However, differential loss rates have to be assumed to reconcile the high birth rates of these incipient de novo genes with the dominance of ancient gene families in individual genomes. Read More

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Native RNA sequencing in fission yeast reveals frequent alternative splicing isoforms.

Genome Res 2022 May 26. Epub 2022 May 26.

Hospital del Mar Medical Research Institute;

The unicellular yeast (fission yeast) retains many of the splicing features observed in humans and is thus an excellent model to study the basic mechanisms of splicing. Nearly half the genes contain introns, but the impact of alternative splicing in gene regulation and proteome diversification remains largely unexplored. Here we leverage Oxford Nanopore Technologies native RNA sequencing (dRNA), as well as ribosome profiling data, to uncover the full range of polyadenylated transcripts and translated open reading frames. Read More

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Unique role for lncRNA HOTAIR in defining depot-specific gene expression patterns in human adipose-derived stem cells.

Genes Dev 2022 May 26. Epub 2022 May 26.

Division of Diabetes Endocrinology and Metabolism, Johns Hopkins University School of Medicine; Institute for Fundamental Biomedical Research, Johns Hopkins All Children's Hospital, St. Petersburg, Florida 33701, USA.

Accumulation of fat above the waist is an important risk factor in developing obesity-related comorbidities independently of BMI or total fat mass. Deciphering the gene regulatory programs of the adipose tissue precursor cells within upper body or abdominal (ABD) and lower body or gluteofemoral (GF) depots is important to understand their differential capacity for lipid accumulation, maturation, and disease risk. Previous studies identified the HOX transcript antisense intergenic RNA (HOTAIR) as a GF-specific lncRNA; however, its role in adipose tissue biology is still unclear. Read More

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Spatial transcriptomics of macrophage infiltration in non-small cell lung cancer reveals determinants of sensitivity and resistance to anti-PD1/PD-L1 antibodies.

J Immunother Cancer 2022 May;10(5)

Department of Medecine, Institut Bergonié, Bordeaux, France

Background: Tumor-associated macrophages (TAMs) having immunosuppressive properties are one of the most abundant immune cells in the tumor microenvironment (TME). Preclinical studies have highlighted the potential role of TAMs in resistance to immune checkpoint blockers (ICBs). Here, we investigated the predictive value of TAM infiltration in patients with non-small cell lung cancer (NSCLC) treated with ICBs and characterized their transcriptomic profiles. Read More

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Bufalin stimulates antitumor immune response by driving tumor-infiltrating macrophage toward M1 phenotype in hepatocellular carcinoma.

J Immunother Cancer 2022 May;10(5)

Institute of Infectious Disease, Shuguang Hospital Affiliated to Shanghai University of Traditional Chinese Medicine, Shanghai, 201203, People's Republic of China

Background: Immunotherapy for hepatocellular carcinoma (HCC) exhibits limited clinical efficacy due to immunosuppressive tumor microenvironment (TME). Tumor-infiltrating macrophages (TIMs) account for the major component in the TME, and the dominance of M2 phenotype over M1 phenotype in the TIMs plays the pivotal role in sustaining the immunosuppressive character. We thus investigate the effect of bufalin on promoting TIMs polarization toward M1 phenotype to improve HCC immunotherapy. Read More

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Efficacy of pembrolizumab in patients with advanced cancer of unknown primary (CUP): a phase 2 non-randomized clinical trial.

J Immunother Cancer 2022 May;10(5)

Investigational Cancer Therapeutics, The University of Texas MD Anderson Cancer Center, Houston, Texas, USA

Background: Cancer of unknown primary (CUP) is an aggressive rare malignancy with limited treatment options. Data regarding clinical activity of immune checkpoint inhibitors in CUP is lacking. Therefore, we evaluated the efficacy of pembrolizumab, a programmed cell death-1 inhibitor, in patients with CUP. Read More

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Transcriptome analysis of CRISPR/Cas9-mediated GPAM in bovine mammary epithelial cell-line unravelled the effects of GPAM gene on lipid metabolism.

Gene 2022 May 23:146574. Epub 2022 May 23.

College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang, Guangdong, 524088, P.R.China. Electronic address:

Glycerol-3-phosphate acyltransferase mitochondrial (GPAM) is an enzyme in animal lipid metabolism pathways that catalyzes the initial and most committed step of glycerolipid biosynthesis. The present study mainly focused on exploring the relationship between the GPAM gene and the lipid metabolism of mammary epithelial cells and the effect of GPAM on the related pathways of lipid metabolism. The GPAM gene was knocked out entirely in bovine mammary epithelial cells(BMECs) using CRISPR/Cas9 technology, and the mechanism by which the GPAM gene regulates lipid metabolism in BMECs was confirmed. Read More

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Using comparative genomics to detect mutations regulating plumage variations in graylag (A. anser) and swan geese (A. cygnoides).

Gene 2022 May 23:146612. Epub 2022 May 23.

Institute of Animal Husbandry & Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai, 201106, P.R. China. Electronic address:

Although graylag geese (A. anser) showed similar plumages of white, grey, and white with grey patches compared to those in swan geese (A. cygnoides), it was believed the substantial molecular mechanism for plumage variations were different. Read More

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Molecular cloning, characterization, and tissue distribution of c-Myc from blood clam Tegillarca granosa and its role in cadmium-induced stress response.

Gene 2022 May 23:146611. Epub 2022 May 23.

Zhejiang Mariculture Research Institute, Zhejiang Key Lab of Exploitation and Preservation of Coastal Bio-Resource, Wenzhou Key Laboratory of Marine Biological Genetics and Breeding, Wenzhou 325005, China. Electronic address:

Cadmium (Cd) pollution threatens the cultivation of the blood clam Tegillarca granosa (T. granosa) in coastal regions of the East China Sea. The molecular mechanisms regulating Cd stress response and detoxification in blood clams are largely unclear. Read More

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Cancer germline antigen gene MAGEB2 promotes cell invasion and correlates with immune microenvironment and immunotherapeutic efficiency in laryngeal cancer.

Clin Immunol 2022 May 23:109045. Epub 2022 May 23.

Department of Head and Neck Surgery, National Cancer Center, National Clinical Research Center for Cancer, Cancer Hospital & Shenzhen Hospital, Chinese Academy of Medical Sciences and Peking Union Medical College, Shenzhen 518116, Guangdong Province, PR China. Electronic address:

By multiple transcriptome datasets (TCGA, GSE59102, GSE25727, GSE27020 and GSE65858) and multi-omics (RNA-seq, SNP, CNV, DNA methylation) in-depth analysis, we found that cancer germline antigen (CGA) family/genes MAGEB2 is involved in the imitation, progression and prognosis in LC as well as correlated positively with lymphatic metastasis and negatively with DNA methylation. Then, in vitro experiment verified that MAGEB2 expression renders significant alteration in LC tissues and cells via immunohistochemical (IHC), qRT-PCR and western blot (WB), and up-regulation of MAGEB2 expression could facilitate the proliferation, migration and invasion of LC cells and vice versa. Subsequently, MAGEB2 knockdown suppressed tumor growth and lung metastasis in vivo animal experiment, while MAGEB2 overexpression promoted tumor growth and lung metastasis. Read More

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Loss of CD226 protects apolipoprotein E-deficient mice from diet-induced atherosclerosis.

Biochim Biophys Acta Mol Basis Dis 2022 May 23:166452. Epub 2022 May 23.

Institute of Medical Research, Northwestern Polytechnical University, 127 West Youyi Road, Xi'an, Shaanxi 710072, China; Department of Immunology, Fourth Military Medical University, 169 West Changle Road, Xi'an, Shaanxi 710032, China. Electronic address:

CD226 is a costimulatory molecule that regulates immune cell functions in T cells, natural killer cells, and macrophages. Because macrophage-derived foam cell formation is a crucial factor contributing to the development of atherosclerosis, we aimed to evaluate the potential roles of CD226 in the pathogenesis of atherosclerosis. The effects of CD226 on atherosclerosis were investigated in CD226 and apolipoprotein E double-knockout (CD226 ApoE) mice fed with a high-cholesterol atherogenic diet. Read More

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Low specific growth rate and temperature in fed-batch cultures of a beta-propeller phytase producing Pichia pastoris strain under GAP promoter trigger increased KAR2 and PSA1-1 gene expression yielding enhanced extracellular productivity.

J Biotechnol 2022 May 23. Epub 2022 May 23.

Universidad Autónoma de Nuevo León, UANL, Facultad de Ciencias Biológicas, Instituto de Biotecnología, 66450 San Nicolás de los Garza, N.L. México. Electronic address:

Previously, we showed that the methylotrophic yeast Pichia pastoris (syn. Komagataella phaffii) could produce and secrete the beta-propeller phytase FTEII in an active form under the control of the AOX1 promoter and methanol as the inductor. In this work, we engineered P. Read More

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The inhibitory effects and underlying mechanism of high ammonia stress on sulfide-driven denitrification process.

Chemosphere 2022 May 23:135093. Epub 2022 May 23.

College of Chemical and Biological Engineering, Key Laboratory of Biomass Chemical Engineering of Ministry of Education, Zhejiang University, Hangzhou, 310027, China; Institute of Zhejiang University-Quzhou, Quzhou, 324000, China. Electronic address:

Sulfide-driven denitrification (SD) process has been widely studied for treating wastewater containing sulfate and ammonia in recent years. But influence of high ammonia stress on the SD process and microbial community remained unclear. In this work, a series of tests were conducted to investigate effects of different ammonia stress (200-3000 mg-total ammonia nitrogen (TAN)/L) on denitrification efficiency, byproduct accumulation and microbial community of the SD process. Read More

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Promotion of corneal angiogenesis by sensory neuron-derived calcitonin gene-related peptide.

Exp Eye Res 2022 May 23:109125. Epub 2022 May 23.

Schepens Eye Research Institute of Massachusetts Eye and Ear, Department of Ophthalmology, Harvard Medical School, Boston, MA, USA. Electronic address:

The normal cornea has no blood vessels but has abundant innervation. There is emerging evidence that sensory nerves, originated from the trigeminal ganglion (TG) neurons, play a key role in corneal angiogenesis. In the current study, we examined the role of TG sensory neuron-derived calcitonin gene-related peptide (CGRP) in promoting corneal neovascularization (CNV). Read More

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Tenofovir disoproxil fumarate-mediated γ-globin induction is correlated with the suppression of trans-acting factors in CD34 progenitor cells: A role in the reactivation of fetal hemoglobin.

Eur J Pharmacol 2022 May 23:175036. Epub 2022 May 23.

Panjwani Center for Molecular Medicine and Drug Research, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan; H.E.J. Research Institute of Chemistry, International Center for Chemical and Biological Sciences, University of Karachi, Karachi, 75270, Pakistan. Electronic address:

Sickle-cell disease (SCD) and β-thalassemia are public health issues that affect people all over the world. Fetal hemoglobin (HbF) induction is a molecular intervention, including hydroxyurea, which has made an effort to improve current treatment. Tenofovir disoproxil fumarate (TDF) is formerly reported with improving levels of hemoglobin, mean corpuscular hemoglobin (MCH), and mean corpuscular volume (MCV). Read More

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A Novel LncRNA PTH-AS Upregulates Interferon-Related DNA damage resistance Signature genes and Promotes Metastasis in Human Breast Cancer Xenografts.

J Biol Chem 2022 May 23:102065. Epub 2022 May 23.

Department of Biochemistry, Teikyo University School of Medicine, 2-11-1 Kaga, Itabashi-ku, Tokyo 173-8605, Japan.

Long non-coding RNAs (lncRNAs) are important tissue-specific regulators of gene expression, and their dysregulation can induce aberrant gene expression leading to various pathological conditions, including cancer. Although many lncRNAs have been discovered by computational analysis, most of these are as yet unannotated. Herein, we describe the nature and function of a novel lncRNA detected downstream of the human parathyroid hormone (PTH) gene in both extremely rare ectopic PTH-producing retroperitoneal malignant fibrous histiocytoma and parathyroid tumors with PTH overproduction. Read More

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Mice heterozygous for a null mutation of Cpe show reduced expression of carboxypeptidase E mRNA and enzyme activity but normal physiology, behavior, and levels of neuropeptides.

Brain Res 2022 May 23:147951. Epub 2022 May 23.

Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, NY, NY, 10029. Electronic address:

Carboxypeptidase E (CPE) is an essential enzyme that contributes to the biosynthesis of the vast majority of neuropeptides and peptide hormones. There are several reports claiming that small decreases in CPE activity cause physiological changes in animals and/or cultured cells, but these studies did not provide evidence that neuropeptide levels were affected by decreased CPE activity. In the present study, we tested if CPE is a rate-limiting enzyme in neuropeptide production using CpeNeo mice, which contain a neomycin cassette within the Cpe gene that eliminates enzyme expression. Read More

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Hypothalamic response with PKA/CREB signaling is associated with direct cerebroventricular administration of bombesin-induced scratching.

Brain Res 2022 May 23:147950. Epub 2022 May 23.

State Key Laboratory of Toxicology and Medical Countermeasures, Beijing Institute of Pharmacology and Toxicology, Beijing 100850, China. Electronic address:

Bombesin (BN) is an itch-specific mediator that causes intense itch-scratching activity in mammals. Although most examinations of BN-induced itch processing have focused on the spinal cord, the involvement of central nervous system mechanisms remains unclear. Here, we investigated how relationships among hypothalamic regions regulate BN-mediated itch-scratch processes. Read More

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Comprehensive analysis of expression profiles and prognosis of TRIM genes in human kidney clear cell carcinoma.

Aging (Albany NY) 2022 May 26;14(undefined). Epub 2022 May 26.

The Department of Urology, The First Hospital of Huzhou, Zhejiang Province, China.

Objective: To determine survival rates and the underlying mechanism of genes in the TRIM family in Kidney Clear Cell Carcinoma (KIRC).

Methods: Transcriptional and survival data of TRIM genes in KIRC patients were retrieved from the UCSC Xena, and GEPIA databases. The function of TRIM genes in KIRC was investigated, focusing on potential ubiquitination, miRNAs regulation, and enrichment analysis. Read More

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Fluoride exposure induces lysosomal dysfunction unveiled by an integrated transcriptomic and metabolomic study in bone marrow mesenchymal stem cells.

Ecotoxicol Environ Saf 2022 May 23;239:113672. Epub 2022 May 23.

Department of Occupational Health (Key Laboratory of Electromagnetic Radiation Protection, Ministry of Education), Third Military Medical University, Chongqing, China. Electronic address:

Fluoride has received much attention for its predominant bone toxicity in the human body. However, the toxic mechanism of bone injury caused by fluoride exposure remains largely unclear. Bone marrow mesenchymal stem cells (BMSCs) are widely used as model cells for evaluating bone toxicity after environmental toxicant exposure. Read More

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Melatonin enhances the antioxidant capacity to rescue the honey bee Apis mellifera from the ecotoxicological effects caused by environmental imidacloprid.

Ecotoxicol Environ Saf 2022 May 23;239:113622. Epub 2022 May 23.

College of Life Sciences, Chongqing Normal University, Chongqing, China; Chongqing Key Laboratory of Microsporidia Infection and Control, China; The State Key Laboratory of Silkworm Genome Biology, Southwest University, Chongqing, China.

Imidacloprid severely poisons the nontarget insect honey bee Apis mellifera. Few treatments are available to mitigate the adverse effects of imidacloprid. The primary concern is that the molecular understanding of imidacloprid toxicity is not comprehensive enough. Read More

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Pathophysiologic and clinical implications of molecular profiles resultant from deletion 5q.

EBioMedicine 2022 May 23;80:104059. Epub 2022 May 23.

Department of Translational Hematology and Oncology Research, Lerner Research Institute Cleveland Clinic, Taussig Cancer Institute, 9500 Euclid Avenue, Cleveland, OH 44195, USA. Electronic address:

Background: Haploinsufficiency (HI) resulting from deletion of the long arm of chromosome 5 [del(5q)] and the accompanied loss of heterozygosity are likely key pathogenic factors in del(5q) myeloid neoplasia (MN) although the consequences of del(5q) have not been yet clarified.

Methods: Here, we explored mutations, gene expression and clinical phenotypes of 388 del(5q) vs. 841 diploid cases with MN [82% myelodysplastic syndromes (MDS)]. Read More

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Defense responses induced by ulvan in wheat against powdery mildew caused by Blumeria graminis f. sp. tritici.

Plant Physiol Biochem 2022 May 14;184:14-25. Epub 2022 May 14.

Université du Littoral Côte d'Opale, Unité de Chimie Environnementale et Interactions sur le Vivant (EA 4492), SFR Condorcet FR CNRS 3417, CS 80699, F-62228, Calais CEDEX, France. Electronic address:

Ulvan is a water-soluble sulfated heteropolysaccharide extracted from the cell walls of the green seaweeds Ulva spp. This polysaccharide is known to induce resistance and protect plants against a broad range of plant pathogenic fungi, such as Blumeria graminis f. sp. Read More

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Voluntary physical activity mitigates alveolar bone loss in mice with ligature-induced experimental periodontitis.

Arch Oral Biol 2022 May 11;140:105451. Epub 2022 May 11.

Health Sciences Department, Federal University of Lavras (UFLA), Lavras, Minas Gerais, Brazil. Electronic address:

Objective: To investigate the effect of voluntary physical activity (VPA) on inflammatory profile and the progression of experimental periodontal disease (PD) in mice.

Methods: Male C57BL/6 mice were randomly distributed into Control; VPA; PD and PD/VPA groups. We registered VPA (total volume of revolutions) and average speed (revolutions/minute) in a free running wheel for 30 days. Read More

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A 2-bp deletion mutation in gene leading to lysosomal acid sphingomyelinase deficiency in a Chinese consanguineous pedigree.

J Pediatr Endocrinol Metab 2022 May 27. Epub 2022 May 27.

Prenatal Diagnosis Department, Chengdu Women's and Children's Central Hospital, School of Medicine, University of Electronic Science and Technology of China, Chengdu, China.

Background: Niemann-Pick disease type A (NPDA, MIM: 257200) is an autosomal recessive sphingolipidosis caused by lysosomal acid sphingomyelinase (ASM) deficiency. A cluster of genes located at chromosome 11p15 have been reported to be imprinted genes, such as TSSC5, TSSC3, and ZNF215 that flanking SMPD1 gene. It was reported by a few recent studies that SMPD1 gene was paternally imprinted and maternally preferentially expressed. Read More

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Down-Regulating Scar Formation by Microneedles Directly a Mechanical Communication Pathway.

ACS Nano 2022 May 26. Epub 2022 May 26.

Institute of Burn Research, State Key Laboratory of Trauma, Burn and Combined Injury, Southwest Hospital, Third Military Medical University (Army Medical University), Chongqing 400038, China.

Excessive extracellular matrix deposition drives fibroblasts into a state of high mechanical stress, exacerbating pathological fibrosis and hypertrophic scar formation, leading to tissue dysfunction. This study reports a minimally invasive and convenient approach to obtaining scarless tissue using a silk fibroin microneedle patch (SF MNs). We found that by tuning the MN size and density only, the biocompatible MNs significantly decreased the scar elevation index in the rabbit ear hypertrophic scar model and increased ultimate tensile strength close to regular skin. Read More

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Spatial and Transcriptomic Analysis of Perineural Invasion in Oral Cancer.

Clin Cancer Res 2022 May 26. Epub 2022 May 26.

University of Michigan School of Dentistry, Ann Arbor, Michigan, United States.

Purpose: Perineural invasion (PNI), a common occurrence in oral squamous cell carcinomas, is associated with poor survival. Consequently, these tumors are treated aggressively. However, diagnostic criteria of PNI vary and its role as an independent predictor of prognosis has not been established. Read More

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Measuring the tail: Methods for poly(A) tail profiling.

Wiley Interdiscip Rev RNA 2022 May 26:e1737. Epub 2022 May 26.

Institute of Genetics and Biotechnology, Faculty of Biology, University of Warsaw, Warsaw, Poland.

The 3'-end poly(A) tail is an important and potent feature of most mRNA molecules that affects mRNA fate and translation efficiency. Polyadenylation is a posttranscriptional process that occurs in the nucleus by canonical poly(A) polymerases (PAPs). In some specific instances, the poly(A) tail can also be extended in the cytoplasm by noncanonical poly(A) polymerases (ncPAPs). Read More

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Shambhala-2: A Protocol for Uniformly Shaped Harmonization of Gene Expression Profiles of Various Formats.

Curr Protoc 2022 May;2(5):e444

Moscow Institute of Physics and Technology, Dolgoprudny, Moscow Region, Russia.

Uniformly shaped harmonization of gene expression profiles is central for the simultaneous comparison of multiple gene expression datasets. It is expected to operate with the gene expression data obtained using various experimental methods and equipment, and to return harmonized profiles in a uniform shape. Such uniformly shaped expression profiles from different initial datasets can be further compared directly. Read More

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