keyword
https://read.qxmd.com/read/38482423/-nf2-is-a-candidate-diagnosis-prognostic-and-immunotherapeutic-biomarker-a-systematic-pan-cancer-analysis
#21
JOURNAL ARTICLE
Honglu Zhang, Jiyong Liu
BACKGROUND: Neurofibromin 2 ( NF2 ) regulates diverse cellular events such as transcription, translation, ubiquitination, and micro-RNA biosynthesis. Previous evidence revealed that aberrant expression of NF2 contributes to tumorigenesis in mesothelioma, meningioma, and breast cancer. However, there is no comprehensive pan-cancer analysis to explore NF2 's function in cancer diagnosis, prognosis, and immunological prediction. METHODS: By extensive use of data profiles from The Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx) project, Cancer Cell Line Encyclopedia (CCLE), CIBERSORT, Human Protein Atlas (HPA), and cBioPortal, we employed various bioinformatics methods to explore the role of NF2 in pan-cancer, including analyzing the association between NF2 and tumor diagnosis, prognosis, immune cell infiltration, tumor mutational burden (TMB), and microsatellite instability (MSI)...
February 29, 2024: Translational Cancer Research
https://read.qxmd.com/read/38477393/raman-micro-spectroscopy-as-a-tool-to-study-immunometabolism
#22
JOURNAL ARTICLE
Jiabao Xu, Karl J Morten
In the past two decades, immunometabolism has emerged as a crucial field, unraveling the intricate molecular connections between cellular metabolism and immune function across various cell types, tissues, and diseases. This review explores the insights gained from studies using the emerging technology, Raman micro-spectroscopy, to investigate immunometabolism. Raman micro-spectroscopy provides an exciting opportunity to directly study metabolism at the single cell level where it can be combined with other Raman-based technologies and platforms such as single cell RNA sequencing...
March 13, 2024: Biochemical Society Transactions
https://read.qxmd.com/read/38475968/large-scale-bioreactor-production-of-extracellular-vesicles-from-mesenchymal-stromal-cells-for-treatment-of-acute-radiation-syndrome
#23
JOURNAL ARTICLE
John A Kink, Michael A Bellio, Matthew H Forsberg, Alexandra Lobo, Anna S Thickens, Bryson M Lewis, Irene M Ong, Aisha Khan, Christian M Capitini, Peiman Hematti
BACKGROUND: Hematopoietic acute radiation syndrome (H-ARS) occurring after exposure to ionizing radiation damages bone marrow causing cytopenias, increasing susceptibility to infections and death. We and others have shown that cellular therapies like human mesenchymal stromal cells (MSCs), or monocytes/macrophages educated ex-vivo with extracellular vesicles (EVs) from MSCs were effective in a lethal H-ARS mouse model. However, given the complexity of generating cellular therapies and the potential risks of using allogeneic products, development of an "off-the-shelf" cell-free alternative like EVs may have utility in conditions like H-ARS that require rapid deployment of available therapeutics...
March 13, 2024: Stem Cell Research & Therapy
https://read.qxmd.com/read/38473229/implications-in-cancer-of-nuclear-micro-rnas-long-non-coding-rnas-and-circular-rnas-bound-by-prc2-and-fus
#24
REVIEW
Guruprasadh Swaminathan, Diana G Rogel-Ayala, Amine Armich, Guillermo Barreto
The eukaryotic genome is mainly transcribed into non-coding RNAs (ncRNAs), including different RNA biotypes, such as micro RNAs (miRNAs), long non-coding RNAs (lncRNAs), and circular RNAs (circRNAs), among others. Although miRNAs are assumed to act primarily in the cytosol, mature miRNAs have been reported and functionally characterized in the nuclei of different cells. Further, lncRNAs are important regulators of different biological processes in the cell nucleus as part of different ribonucleoprotein complexes...
February 21, 2024: Cancers
https://read.qxmd.com/read/38466505/platelet-derived-microvesicles-mediate-cardiomyocyte-ferroptosis-by-transferring-acsl1-during-acute-myocardial-infarction
#25
JOURNAL ARTICLE
Yunfeng Zhao, Rui Cui, Ran Du, Chunmei Song, Fei Xie, Lin Ren, Junquan Li
Acute myocardial infarction (AMI) is one of the critical health conditions often caused by the rupture of unstable coronary artery plaque, triggering a series of events, such as platelet activation, thrombus formation, coronary artery blockage, lasted severe ischemia, and hypoxia in cardiomyocytes, and culminating in cell death. Platelet-derived microvesicles (PMVs) act as intermediates for cellular communication. Nevertheless, the role of PMVs in myocardial infarction remains unclear. Initially, AMI-related messenger ribose nucleic acid (mRNA) and micro RNA (miRNA) datasets from the Gene Expression Omnibus (GEO) database were analyzed, specifically focusing on the expressed genes associated with Ferroptosis...
March 11, 2024: Molecular Biotechnology
https://read.qxmd.com/read/38462114/a-bert-based-model-for-the-prediction-of-lncrna-subcellular-localization-in-homo-sapiens
#26
JOURNAL ARTICLE
Zhao-Yue Zhang, Zheng Zhang, Xiucai Ye, Tetsuya Sakurai, Hao Lin
Understanding the subcellular localization of lncRNAs is crucial for comprehending their regulation activities. The conventional detection of lncRNA subcellular location usually uses in situ detection techniques, which are resource intensive. Some machine learning-based algorithms have been proposed for lncRNA subcellular location prediction in mammals. However, due to the low level of conservation of lncRNA sequence, the performance of cross-species models remains unsatisfactory. In this study, we curated a novel dataset containing subcellular location information of lncRNAs in Homo sapiens...
March 8, 2024: International Journal of Biological Macromolecules
https://read.qxmd.com/read/38462040/the-role-and-mechanisms-of-non-coding-rnas-in-diabetic-peripheral-neuropathy
#27
REVIEW
Yiqian He, Ling Qu
Diabetic peripheral neuropathy (DPN) is a complication of diabetes with a high rate of disability. However, current clinical treatments for DPN are suboptimal. Non-coding RNAs (ncRNAs) are a type of RNAs that are not translated into proteins. NcRNAs perform functions that regulate epigenetic modifications, transcriptional or post-transcriptional regulators of proteins, and thus participate in the physiological and pathological processes of the body. NcRNAs play a role in the progress of DPN by affecting the processes of inflammation, oxidative stress, cellular autophagy or apoptosis...
March 8, 2024: Metabolism: Clinical and Experimental
https://read.qxmd.com/read/38459192/glucose-ingestion-before-and-after-resistance-training-sessions-does-not-augment-ribosome-biogenesis-in-healthy-moderately-trained-young-adults
#28
JOURNAL ARTICLE
Kristian Lian, Daniel Hammarström, Håvard Hamarsland, Knut Sindre Mølmen, Sara Christine Moen, Stian Ellefsen
PURPOSE: Resistance training-induced skeletal muscle hypertrophy seems to depend on ribosome biogenesis and content. High glucose treatment may augment ribosome biogenesis through potentiating resistance training-induced adaptations. This was investigated with total RNA and ribosomal RNA abundances as main outcomes, with relevant transcriptional/translational regulators (c-Myc/UBF/rpS6) as a secondary outcome. METHODS: Sixteen healthy, moderately trained individuals [male/female, n = 9/7; age, 24...
March 8, 2024: European Journal of Applied Physiology
https://read.qxmd.com/read/38453824/the-interplay-between-epilepsy-and-parkinson-s-disease-gene-expression-profiling-and-functional-analysis
#29
JOURNAL ARTICLE
Xiaolong Wu, Kailiang Wang, Jingjing Wang, Penghu Wei, Huaqiang Zhang, Yanfeng Yang, Yinchun Huang, Yihe Wang, Wenli Shi, Yongzhi Shan, Guoguang Zhao
The results of many epidemiological studies suggest a bidirectional causality may exist between epilepsy and Parkinson's disease (PD). However, the underlying molecular landscape linking these two diseases remains largely unknown. This study aimed to explore this possible bidirectional causality by identifying differentially expressed genes (DEGs) in each disease as well as their intersection based on two respective disease-related datasets. We performed enrichment analyses and explored immune cell infiltration based on an intersection of the DEGs...
March 7, 2024: Molecular Biotechnology
https://read.qxmd.com/read/38452772/the-interrelation-between-the-high-expression-level-of-mir34a-and-the-trisomic-abortion-materials
#30
JOURNAL ARTICLE
Elvin Kazancioglu, Esra Tug, Mehmet Ali Ergun, Hasan Huseyin Kazan, Meral Yirmibes Karaoguz
AIMS: The underlying mechanism and constitution of spontaneous abortions are complicated and heterogeneous. Many factors, including epigenetic scenarios like micro-ribonucleic acids (miRNAs, MIRs), can additively affect the progression of pregnancy losses. This study aimed to evaluate whether the expression levels of placental inhibitor and/or activator miRNAs had a difference between the numerically abnormal and normal karyotyped spontaneous abortions. METHODS: The case-control study included 100 spontaneous abortion materials consisting of trophoblastic tissues with 42 disomies (controls), 43 aneuploidies (including trisomy 16, 21, 22, and monosomy X), and 15 triploidies...
March 7, 2024: Journal of Obstetrics and Gynaecology Research
https://read.qxmd.com/read/38436559/exploring-mirna-target-gene-pair-detection-in-disease-with-cormit
#31
JOURNAL ARTICLE
Jose Cordoba-Caballero, James R Perkins, Federico García-Criado, Diana Gallego, Alicia Navarro-Sánchez, Mireia Moreno-Estellés, Concepción Garcés, Fernando Bonet, Carlos Romá-Mateo, Rocio Toro, Belén Perez, Pascual Sanz, Matthias Kohl, Elena Rojano, Pedro Seoane, Juan A G Ranea
A wide range of approaches can be used to detect micro RNA (miRNA)-target gene pairs (mTPs) from expression data, differing in the ways the gene and miRNA expression profiles are calculated, combined and correlated. However, there is no clear consensus on which is the best approach across all datasets. Here, we have implemented multiple strategies and applied them to three distinct rare disease datasets that comprise smallRNA-Seq and RNA-Seq data obtained from the same samples, obtaining mTPs related to the disease pathology...
January 22, 2024: Briefings in Bioinformatics
https://read.qxmd.com/read/38425992/inhibition-of-pten-promotes-osteointegration-of-titanium-implants-in-type-2-diabetes-by-enhancing-anti-inflammation-and-osteogenic-capacity-of-adipose-derived-stem-cells
#32
JOURNAL ARTICLE
Guanhua Zhang, Shuang Song, Zijun Chen, Xiangdong Liu, Jian Zheng, Yuxi Wang, Xutao Chen, Yingliang Song
Background: The low osteogenic differentiation potential and attenuated anti-inflammatory effect of adipose-derived stem cells (ADSCs) from animals with type 2 diabetes mellitus (T2DM) limits osseointegration of the implant. However, the underlying mechanisms are not fully understood. Methods: Western blotting and qRT-PCR analyses were performed to investigate the effects of PTEN on the osteogenic capacity of ADSCs of T2DM rats (TADSCs). We conducted animal experiments in T2DM-Sprague Dawley (SD) rats to evaluate the osteogenic capacity of modified TADSC sheets in vivo ...
2024: Frontiers in Bioengineering and Biotechnology
https://read.qxmd.com/read/38425422/multiplex-electrochemical-sensing-platforms-for-the-detection-of-breast-cancer-biomarkers
#33
REVIEW
Connor O'Brien, Chun Keat Khor, Sina Ardalan, Anna Ignaszak
Herein, advancements in electroanalytical devices for the simultaneous detection of diverse breast cancer (BC) markers are demonstrated. This article identifies several important areas of exploration for electrochemical diagnostics and highlights important factors that are pivotal for the successful deployment of novel bioanalytical devices. We have highlighted that the limits of detection (LOD) reported for the multiplex electrochemical biosensor can surpass the sensitivity displayed by current clinical standards such as ELISA, FISH, and PCR...
2024: Frontiers in medical technology
https://read.qxmd.com/read/38419141/high-throughput-host-microbe-single-cell-rna-sequencing-reveals-ferroptosis-associated-heterogeneity-during-acinetobacter-baumannii%C3%A2-infection
#34
JOURNAL ARTICLE
Hongen Meng, Tianyu Zhang, Wang Zhang, Yuyi Zhu, Yingying Yu, Jiaye Chen, Hangfei Chen, Fudi Wang, Yunsong Yu, Xiaoting Hua, Yongcheng Wang
Interactions between host and bacterial cells are integral to human physiology. The complexity of host-microbe interactions extends to different cell types, spatial aspects, and phenotypic heterogeneity, requiring high-resolution approaches to capture their full complexity. The latest breakthroughs in single-cell RNA sequencing (scRNA-seq) have opened up a new era of studies in host-pathogen interactions. Here, we first report a high-throughput cross-species dual scRNA-seq technology by using random primers to simultaneously capture both eukaryotic and bacterial RNAs (scRandom-seq)...
February 28, 2024: Angewandte Chemie
https://read.qxmd.com/read/38417568/iron-overload-increases-the-sensitivity-of-endometriosis-stromal-cells-to-ferroptosis-via-a-prc2-independent-function-of-ezh2
#35
JOURNAL ARTICLE
Yong Luo, Liping Li, Qiwen Hu, Ziyu Zhang, Faying Liu, Yongbao Peng, Yang Zou, Lina Chen
Given the high concentration of iron in the micro-environment of ovarian endometriosis, it is plausible to hypothesize that ectopic endometrial cells may be more susceptible to undergoing ferroptosis. Manipulation of ferroptosis has been explored as a potential therapeutic strategy to treat related diseases. In this study, we examined the impact on ectopic endometrial stromal cells (EESCs) of iron overload and an inducer of ferroptosis. We found that the iron concentration in the ovarian endometriosis was much higher than control samples...
February 27, 2024: International Journal of Biochemistry & Cell Biology
https://read.qxmd.com/read/38417293/prediction-of-immunotherapy-responsiveness-in-melanoma-through-single-cell-sequencing-based-characterization-of-the-tumor-immune-microenvironment
#36
JOURNAL ARTICLE
Yucheng Dong, Zhizhuo Chen, Fan Yang, Jiaxin Wei, Jiuzuo Huang, Xiao Long
Immune checkpoint inhibitors (ICB) therapy have emerged as effective treatments for melanomas. However, the response of melanoma patients to ICB has been highly heterogenous. Here, by analyzing integrated scRNA-seq datasets from melanoma patients, we revealed significant differences in the TiME composition between ICB-resistant and responsive tissues, with resistant or responsive tissues characterized by an abundance of myeloid cells and CD8+ T cells or CD4+ T cell predominance, respectively. Among CD4+ T cells, CD4+ CXCL13+ Tfh-like cells were associated with an immunosuppressive phenotype linked to immune escape-related genes and negative regulation of T cell activation...
February 27, 2024: Translational Oncology
https://read.qxmd.com/read/38412917/plasma-micrornas-as-biomarkers-in-hereditary-angioedema
#37
JOURNAL ARTICLE
Timothy Craig, Kristina Richwine, Faoud T Ishmael
BACKGROUND: Hereditary angioedema (HAE) is an autosomal dominant disease with variable expression. In some families with identical genetic abnormality, the expression can range from several attacks per month to no attacks at all. It is hypothesized that post-transcriptional gene regulation account for the variable expression of the disease. OBJECTIVE: We sought to identify candidate micro-ribonucleic acids (miRNAs) that could play a role in HAE by determining whether miRNAs differentially expressed in HAE vs...
February 25, 2024: Annals of Allergy, Asthma & Immunology
https://read.qxmd.com/read/38408231/ultrafast-sound-production-mechanism-in-one-of-the-smallest-vertebrates
#38
JOURNAL ARTICLE
Verity A N O Cook, Antonia H Groneberg, Maximilian Hoffmann, Mykola Kadobianskyi, Johannes Veith, Lisanne Schulze, Jörg Henninger, Ralf Britz, Benjamin Judkewitz
Motion is the basis of nearly all animal behavior. Evolution has led to some extraordinary specializations of propulsion mechanisms among invertebrates, including the mandibles of the dracula ant and the claw of the pistol shrimp. In contrast, vertebrate skeletal movement is considered to be limited by the speed of muscle, saturating around 250 Hz. Here, we describe the unique propulsion mechanism by which Danionella cerebrum , a miniature cyprinid fish of only 12 mm length, produces high amplitude sounds exceeding 140 dB (re...
March 5, 2024: Proceedings of the National Academy of Sciences of the United States of America
https://read.qxmd.com/read/38404554/identifying-endoplasmic-reticulum-stress-related-genes-as-new-diagnostic-and-prognostic-biomarkers-in-clear-cell-renal-cell-carcinoma
#39
JOURNAL ARTICLE
Haitao Yu, Chunlin Zhang, Xuesong Bai, Hubin Yin, Xinyuan Li, Xiang Zhou, Weiyang He, Youlin Kuang, Xin Gou, Jie Li
BACKGROUND: Clear cell renal cell carcinoma (ccRCC) is one of the most common cancers worldwide, and its incidence is increasing every year. Endoplasmic reticulum stress (ERS) caused by protein misfolding has broad and profound effects on the progression and metastasis of various cancers. Accumulating evidence suggests that ERS is closely related to the occurrence and progression of ccRCC. This study aimed to identify ERS-related genes for evaluating the prognosis of ccRCC. METHODS: Transcriptomic expression profiles were obtained from the Gene Expression Omnibus (GEO) and The Cancer Genome Atlas (TCGA), and clinical data were downloaded from the TCGA...
January 31, 2024: Translational Andrology and Urology
https://read.qxmd.com/read/38399344/carbon-based-nanostructures-as-emerging-materials-for-gene-delivery-applications
#40
REVIEW
Sara Yazdani, Mehrdad Mozaffarian, Gholamreza Pazuki, Naghmeh Hadidi, Ilia Villate-Beitia, Jon Zárate, Gustavo Puras, Jose Luis Pedraz
Gene therapeutics are promising for treating diseases at the genetic level, with some already validated for clinical use. Recently, nanostructures have emerged for the targeted delivery of genetic material. Nanomaterials, exhibiting advantageous properties such as a high surface-to-volume ratio, biocompatibility, facile functionalization, substantial loading capacity, and tunable physicochemical characteristics, are recognized as non-viral vectors in gene therapy applications. Despite progress, current non-viral vectors exhibit notably low gene delivery efficiency...
February 18, 2024: Pharmaceutics
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