37,217 results match your criteria rna profiles

Combining gene expression signature with clinical features for survival stratification of gastric cancer.

Genomics 2021 Jun 12. Epub 2021 Jun 12.

Department of Cell Biology, Zhejiang University School of Medicine, Hangzhou 310058, China; Institute of Gastroenterology, Zhejiang University, Hangzhou 310016, China; Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Hangzhou, Zhejiang 310003, China; Department of Molecular Genetics, University of Toronto, Toronto, ONM5S 1A8, Canada. Electronic address:

The AJCC staging system is considered as the golden standard in clinical practice. However, it remains some pitfalls in assessing the prognosis of gastric cancer (GC) patients with similar clinicopathological characteristics. We aim to develop a new clinic and genetic risk score (CGRS) to improve the prognosis prediction of GC patients. Read More

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RNA sequencing identifies two novel liver-specific long noncoding RNAs with potential diagnostic value in hepatocellular carcinoma.

Biomark Med 2021 Jun 15. Epub 2021 Jun 15.

Department of Epidemiology & Health Statistics, School of Public Health, Guangxi Medical University, Nanning, Guangxi, 530021, PR China.

To explore the expression profiles of long noncoding RNAs (lncRNAs) and identify novel lncRNAs as biomarkers for early diagnosis and therapy of hepatocellular carcinoma (HCC). Expression profiles of lncRNAs and mRNAs in five paired HCC and adjacent normal tissues were obtained by RNA sequencing. Eight lncRNAs, including two novel liver-specific lncRNAs (NONHSAT059247. Read More

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Transcriptome of D14 in vivo x in vitro bovine embryos: is there any difference?

In Vitro Cell Dev Biol Anim 2021 Jun 14. Epub 2021 Jun 14.

University of Brasilia, Animal Science, Merk Millipore /Sigma-Aldrich Brasil, São Paulo, DF, 70910-900, Brazil.

It is well-established that in vitro culture affects quality, gene expression, and epigenetic processes in bovine embryos and that trophectoderm cells are the most susceptible to abnormalities. These changes have been reported as the main factors responsible for losses observed after transfer of in vitro-produced embryos. The present study aimed to investigate the effect of an in vitro system on bovine embryo transcriptional profiles on D14 of development. Read More

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CircASXL1 knockdown represses the progression of colorectal cancer by downregulating GRIK3 expression by sponging miR-1205.

World J Surg Oncol 2021 Jun 14;19(1):176. Epub 2021 Jun 14.

Department of General Surgery, Shanghai Fengxian Central Hospital, No. 6600, Nanfeng Road, Nanqiao New Town, Fengxian District, Shanghai, 201400, China.

Background: Colorectal cancer (CRC) is a common aggressive tumor that poses a heavy burden to human health. An increasing number of studies have reported that circular RNA (circRNA) is involved in the progression of CRC. In this study, the special profiles of circASXL1 (circ_0001136) in CRC progression were revealed. Read More

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Ovary-derived circular RNAs profile analysis during the onset of puberty in gilts.

BMC Genomics 2021 Jun 15;22(1):445. Epub 2021 Jun 15.

Guangdong Laboratory of Lingnan Modern Agriculture, National Engineering Research Center for Breeding Swine Industry, Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, College of Animal Science, South China Agricultural University, 510642, Guangzhou, China.

Background: In mammals, the ovary is the essential system of female reproduction for the onset of puberty, and the abnormal puberty has negative outcomes on health. CircRNA is a non-coding RNA produced by non-canonical alternative splicing (AS). Several studies have reported that circRNA is involved in the gene regulation and plays an important role in some human diseases. Read More

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Free energy landscape of RNA binding dynamics in start codon recognition by eukaryotic ribosomal pre-initiation complex.

PLoS Comput Biol 2021 Jun 14;17(6):e1009068. Epub 2021 Jun 14.

Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, Japan.

Specific interaction between the start codon, 5'-AUG-3', and the anticodon, 5'-CAU-3', ensures accurate initiation of translation. Recent studies show that several near-cognate start codons (e.g. Read More

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Conformational changes in three-dimensional chromatin structure in after phytoplasma infection.

Phytopathology 2021 Jun 14. Epub 2021 Jun 14.

Beijing, China;

Higher-order chromatin structures play important roles in regulating multiple biological processes, growth and development, biotic and abiotic stress response. However, little is known about three-dimensional chromatin structures in Paulownia, or about whole-genome chromatin conformational changes that occur in response to Paulownia witches' broom (PaWB) disease. We used high-throughput chromosome conformation capture (Hi-C) to obtain genome-wide profiles of chromatin conformation in healthy and phytoplasma-infected genome. Read More

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Identification and Verification of a 17 Immune-Related Gene Pair Prognostic Signature for Colon Cancer.

Biomed Res Int 2021 22;2021:6057948. Epub 2021 May 22.

Departments of Gastrointestinal Surgery, The Second Affiliated Hospital of Dalian Medical University, Dalian 116023, China.

Background: Colon cancer (CC) is a malignant tumor with a high incidence and poor prognosis. Accumulating evidence shows that the immune signature plays an important role in the tumorigenesis, progression, and prognosis of CC. Our study is aimed at establishing a novel robust immune-related gene pair signature for predicting the prognosis of CC. Read More

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Gene Expression Profiles of Circular RNAs and MicroRNAs in Chronic Rhinosinusitis With Nasal Polyps.

Front Mol Biosci 2021 28;8:643504. Epub 2021 May 28.

Department of Otorhinolaryngology Head and Neck Surgery, The First Affiliated Hospital of Nanchang University, Nanchang, China.

Chronic rhinosinusitis (CRS) is often classified primarily on the basis of the absence or presence of nasal polyps (NPs), that is, as CRS with nasal polyps (CRSwNP) or CRS without nasal polyps (CRSsNP). Additionally, according to the percentage of eosinophils, CRSwNP can be further divided into eosinophilic CRSwNP (ECRSwNP) and non-ECRSwNP. CRSwNP is a significant public health problem with a considerable socioeconomic burden. Read More

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Early prediction of COVID-19 severity using extracellular vesicle COPB2.

J Extracell Vesicles 2021 Jun 2;10(8):e12092. Epub 2021 Jun 2.

Department of Molecular and Cellular Medicine Institute of Medical Science Tokyo Medical University Tokyo Japan.

The clinical manifestations of COVID-19 vary broadly, ranging from asymptomatic infection to acute respiratory failure and death. But the predictive biomarkers for characterizing the variability are still lacking. Since emerging evidence indicates that extracellular vesicles (EVs) and extracellular RNAs (exRNAs) are functionally involved in a number of pathological processes, we hypothesize that these extracellular components may be key determinants and/or predictors of COVID-19 severity. Read More

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Gene Instability-Related lncRNA Prognostic Model of Melanoma Patients via Machine Learning Strategy.

J Oncol 2021 25;2021:5582920. Epub 2021 May 25.

Department of Dermatology, The First Hospital of China Medical University, National Health Commission Key Laboratory of Immunodermatology, Key Laboratory of Immunodermatology of Ministry of Education, Shenyang, Liaoning, China.

Background: Melanoma is a common tumor characterized by a high mortality rate in its late stage. After metastasis, current treatment methods are relatively ineffective. Many studies have shown that long noncoding RNA (lncRNA) may participate in gene mutation and genomic instability in cancer. Read More

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Superficial CD34-Positive Fibroblastic Tumor and PRDM10-rearranged Soft Tissue tumor are overlapping entities: a comprehensive study of 20 cases.

Histopathology 2021 Jun 14. Epub 2021 Jun 14.

Department of Biopathology, Institut Bergonie, Bordeaux, France.

Introduction: Superficial CD34-Positive Fibroblastic Tumor (SCD34FT) and PRDM10-rearranged soft tissue Tumor (PRDM10-STT) are rare mesenchymal tumors. These lesions have clinicopathological similarities, but their relationship remains controversial. This study aimed to characterize a series of cases of SCD34FT and PRDM10-STT. Read More

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Full-length transcriptome sequence analysis of Eimeria necatrix unsporulated oocysts and sporozoites identifies genes involved in cellular invasion.

Vet Parasitol 2021 Jun 2;296:109480. Epub 2021 Jun 2.

College of Veterinary Medicine, Yangzhou University, Yangzhou, 225009, China; Jiangsu Co-innovation Center for Prevention and Control of Important Animal Infectious Diseases and Zoonoses, Yangzhou University, Yangzhou, 225009, China; Jiangsu Key Laboratory of Zoonosis, Yangzhou University, Yangzhou, 225009, China. Electronic address:

Eimeria necatrix is one of the most pathogenic chicken coccidia and causes avian coccidiosis, an enteric disease of major economic importance worldwide. Eimeria parasites have complex developmental life cycles, with an exogenous phase in the environment and an endogenous phase in the chicken intestine. Oocysts excreted by chickens rapidly undergo meiosis and cell division to form eight haploid sporozoites (SZ). Read More

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Single-cell RNA sequencing reveals the mechanism of sonodynamic therapy combined with a RAS inhibitor in the setting of hepatocellular carcinoma.

J Nanobiotechnology 2021 Jun 12;19(1):177. Epub 2021 Jun 12.

Department of Ultrasound, Harbin Medical University Cancer Hospital, No.150, Haping Road, Nangang District, Harbin, 150081, Heilongjiang, China.

Background: Ras activation is a frequent event in hepatocellular carcinoma (HCC). Combining a RAS inhibitor with traditional clinical therapeutics might be hampered by a variety of side effects, thus hindering further clinical translation. Herein, we report on integrating an IR820 nanocapsule-augmented sonodynamic therapy (SDT) with the RAS inhibitor farnesyl-thiosalicylic acid (FTS). Read More

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IL-10 and TGF-β cytokines decrease immune activation during normothermic ex vivo machine perfusion of the rat liver.

Liver Transpl 2021 Jun 12. Epub 2021 Jun 12.

Department of Surgery, Division of Transplantation, University of Wisconsin, School of Medicine and Public Health, Madison.

Background: Normothermic ex vivo liver perfusion (NEVLP) is a novel system for organ preservation which may improve over static cold storage (CS) clinically and offers the chance for graft modification prior to transplantation. Although recent studies have shown the presence of inflammatory molecules during perfusion, none have yet shown the effects of NEVLP on liver-resident immune cell activation. We investigated the effects of NEVLP on liver-resident immune cell activation and assessed the ability of anti-inflammatory cytokines IL-10 and TGF-β to improve organ function and reduce immune activation during perfusion. Read More

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Likelihood-based tests for detecting circadian rhythmicity and differential circadian patterns in transcriptomic applications.

Brief Bioinform 2021 Jun 12. Epub 2021 Jun 12.

Department of Biostatistics at the University of Florida, Gainesville, FL, 32608, USA.

Circadian rhythmicity in transcriptomic profiles has been shown in many physiological processes, and the disruption of circadian patterns has been found to associate with several diseases. In this paper, we developed a series of likelihood-based methods to detect (i) circadian rhythmicity (denoted as LR_rhythmicity) and (ii) differential circadian patterns comparing two experimental conditions (denoted as LR_diff). In terms of circadian rhythmicity detection, we demonstrated that our proposed LR_rhythmicity could better control the type I error rate compared to existing methods under a wide variety of simulation settings. Read More

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Human induced pluripotent stem cell derived hepatocytes provide insights on parenteral nutrition associated cholestasis in the immature liver.

Sci Rep 2021 Jun 11;11(1):12386. Epub 2021 Jun 11.

Department of Pediatrics, Medical College of Wisconsin, 999 N. 92 Street, PO Box 1997, Milwaukee, WI, 53226, USA.

Parenteral nutrition-associated cholestasis (PNAC) significantly limits the safety of intravenous parenteral nutrition (PN). Critically ill infants are highly vulnerable to PNAC-related morbidity and mortality, however the impact of hepatic immaturity on PNAC is poorly understood. We examined developmental differences between fetal/infant and adult livers, and used human induced pluripotent stem cell-derived hepatocyte-like cells (iHLC) to gain insights into the contribution of development to altered sterol metabolism and PNAC. Read More

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Identification of lymphocyte cell-specific protein-tyrosine kinase (LCK) as a driver for invasion and migration of oral cancer by tumor heterogeneity exploitation.

Mol Cancer 2021 Jun 11;20(1):88. Epub 2021 Jun 11.

Junior Research Group 'RNA biology and pathogenesis', Faculty of Medicine, Martin Luther University Halle-Wittenberg, 06120, Halle, Germany.

Background: Cancer metastases are the main cause of lethality. The five-year survival rate for patients diagnosed with advanced stage oral cancer is 30%. Hence, the identification of novel therapeutic targets is an urgent need. Read More

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Microscopic examination of spatial transcriptome using Seq-Scope.

Cell 2021 Jun 7. Epub 2021 Jun 7.

Department of Molecular and Integrative Physiology, University of Michigan Medical School, Ann Arbor, MI 48109, USA. Electronic address:

Spatial barcoding technologies have the potential to reveal histological details of transcriptomic profiles; however, they are currently limited by their low resolution. Here, we report Seq-Scope, a spatial barcoding technology with a resolution comparable to an optical microscope. Seq-Scope is based on a solid-phase amplification of randomly barcoded single-molecule oligonucleotides using an Illumina sequencing platform. Read More

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Efficient representations of tumor diversity with paired DNA-RNA aberrations.

PLoS Comput Biol 2021 Jun 11;17(6):e1008944. Epub 2021 Jun 11.

Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, Maryland, United States of America.

Cancer cells display massive dysregulation of key regulatory pathways due to now well-catalogued mutations and other DNA-related aberrations. Moreover, enormous heterogeneity has been commonly observed in the identity, frequency and location of these aberrations across individuals with the same cancer type or subtype, and this variation naturally propagates to the transcriptome, resulting in myriad types of dysregulated gene expression programs. Many have argued that a more integrative and quantitative analysis of heterogeneity of DNA and RNA molecular profiles may be necessary for designing more systematic explorations of alternative therapies and improving predictive accuracy. Read More

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RNA-sequencing of peripheral blood circular RNAs in Parkinson disease.

Medicine (Baltimore) 2021 Jun;100(23):e25888

Department of Neurology, The Affiliated Hospital of Jining Medical University.

Background: Circular RNAs (circRNAs) play an important role in many neurological diseases and can serve as biomarkers for these diseases. However, the information about circRNAs in Parkinson disease (PD) remained limited. In this study, we aimed to determine the circRNAs expression profile in PD patients and discuss the significance of circRNAs in the diagnosis of PD. Read More

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Expression profiles and functional analysis of plasma tRNA-derived small RNAs in children with fulminant myocarditis.

Epigenomics 2021 Jun 11. Epub 2021 Jun 11.

Department of Pediatric Cardiology, Shandong Provincial Hospital Affiliated to Shandong First Medical University, Jinan, Shandong 250021, PR China.

Fulminant myocarditis (FM) has neither validated biomarkers nor well-established therapy. Roles of tRNA-derived small RNAs (tsRNAs) in FM remain unknown. Small RNA sequencing was conducted in plasma from children with FM during acute and convalescent phase and matched healthy volunteers. Read More

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Integrating miRNA and mRNA Profiling to Assess the Potential miRNA-mRNA Modules Linked With Testicular Immune Homeostasis in Sheep.

Front Vet Sci 2021 25;8:647153. Epub 2021 May 25.

College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.

Beyond its well-known role in spermatogenesis and androgen production, mammalian testes are increasingly recognized as an immune-privileged organ for protecting autoantigenic germ cells, especially meiotic and postmeiotic germ cells, from systemic immune responses. Despite its importance, the molecular mechanisms underlying this regulation in mammals, including sheep, are far from known. In this study, we searched for the genes associated with testicular immune privilege and assessed their possible modulating mechanisms by analyzing systematic profiling of mRNAs and miRNAs on testicular tissues derived from prepubertal and postpubertal Tibetan sheep acquired by RNA sequencing. Read More

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The Presence of Circulating Nucleated Red Blood Cells Is Associated With Disease Severity in Patients of Hemorrhagic Fever With Renal Syndrome.

Front Med (Lausanne) 2021 25;8:665410. Epub 2021 May 25.

Department of Immunology, Basic Medicine School, Air Force Medical University, Xi'an, China.

Hemorrhagic fever with renal syndrome (HFRS) is a regional infectious disease of epidemic potential caused by the Hantaan virus (HTNV). Red blood cells (RBCs) are the major components of peripheral blood. However, pathological changes in RBCs and the underlying mechanisms during HTNV infection remain largely unclear. Read More

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Gene Expression Profile of the Human Colorectal Carcinoma LoVo Cells Treated With Sporamin and Thapsigargin.

Front Oncol 2021 25;11:621462. Epub 2021 May 25.

School of Public Health, Capital Medical University (CMU), Beijing, China.

Sporamin, a proteinase inhibitor isolated from the sweet potato (), has shown promising anticancer effect against colorectal cancer (CRC) and but its mechanisms of action are poorly understood. In the present study, high throughput RNA sequencing (RNA-seq) technology was applied to explore the transcriptomic changes induced by sporamin in the presence of thapsigargin (TG), a non-12-O-tetradecanolphorbol-13-acetate type cancer promoter, in the LoVo human CRC cells. Cellular total RNA was extracted from the cells after they were treated with vehicle (CTL), 1 μM of thapsigargin (TG), or 1 μM of TG plus 30 μM of sporamin (TGSP) for 24 h. Read More

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Analysis of ceRNA networks and identification of potential drug targets for drug-resistant leukemia cell K562/ADR.

PeerJ 2021 25;9:e11429. Epub 2021 May 25.

Department of Clinical Laboratory, Shenzhen Traditional Chinese Medicine Hospital, Shenzhen, Guangdong, China.

Background: Drug resistance is the main obstacle in the treatment of leukemia. As a member of the competitive endogenous RNA (ceRNA) mechanism, underlying roles of lncRNA are rarely reported in drug-resistant leukemia cells.

Methods: The gene expression profiles of lncRNAs and mRNAs in doxorubicin-resistant K562/ADR and sensitive K562 cells were established by RNA sequencing (RNA-seq). Read More

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Identifying molecular targets for reverse aging using integrated network analysis of transcriptomic and epigenomic changes during aging.

Sci Rep 2021 Jun 10;11(1):12317. Epub 2021 Jun 10.

Department of Bio and Brain Engineering, Korea Advanced Institute of Science and Technology (KAIST), Daejeon, 34141, Republic of Korea.

Aging is associated with widespread physiological changes, including skeletal muscle weakening, neuron system degeneration, hair loss, and skin wrinkling. Previous studies have identified numerous molecular biomarkers involved in these changes, but their regulatory mechanisms and functional repercussions remain elusive. In this study, we conducted next-generation sequencing of DNA methylation and RNA sequencing of blood samples from 51 healthy adults between 20 and 74 years of age and identified aging-related epigenetic and transcriptomic biomarkers. Read More

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Comprehensive Genomic and Transcriptomic Analysis for Guiding Therapeutic Decisions in Patients with Rare Cancers.

Cancer Discov 2021 Jun 10. Epub 2021 Jun 10.

Omics IT and Data Management Core Facility, German Cancer Research Center.

The clinical relevance of comprehensive molecular analysis in rare cancers is not established. We analyzed the molecular profiles and clinical outcomes of 1,310 patients (rare cancers, 75.5%) enrolled in a prospective observational study by the German Cancer Consortium that applies whole-genome/exome and RNA sequencing to inform the care of adults with incurable cancers. Read More

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Comparison of renal histopathology and gene expression profiles between severe COVID-19 and bacterial sepsis in critically ill patients.

Crit Care 2021 06 10;25(1):202. Epub 2021 Jun 10.

Department of Critical Care, University of Groningen, University Medical Center Groningen, Hanzeplein 1, 9713 GZ, Groningen, The Netherlands.

Background: The mechanisms driving acute kidney injury (AKI) in critically ill COVID-19 patients are unclear. We collected kidney biopsies from COVID-19 AKI patients within 30 min after death in order to examine the histopathology and perform mRNA expression analysis of genes associated with renal injury.

Methods: This study involved histopathology and mRNA analyses of postmortem kidney biopsies collected from patients with COVID-19 (n = 6) and bacterial sepsis (n = 27). Read More

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CircRNA NALCN acts as an miR-493-3p sponge to regulate PTEN expression and inhibit glioma progression.

Cancer Cell Int 2021 Jun 10;21(1):307. Epub 2021 Jun 10.

Department of Neurosurgery, Xiangya Hospital, Central South University, Changsha, Hunan, China.

Background: An increasing number of studies have shown that circular RNAs (circRNAs) play important roles in the regulation of tumor progression. Therefore, we explored the expression characteristics, function, and related mechanism of the newly identified circNALCN in glioma.

Methods: RNA sequencing was used to analyze the expression profiles of circRNAs in brain tissue from five glioma cases and four normal controls. Read More

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