keyword
https://read.qxmd.com/read/38498023/tyr352-as-a-predominant-phosphosite-in-the-understudied-kinase-and-molecular-target-hipk1-implications-for-cancer-therapy
#1
JOURNAL ARTICLE
Diya Sanjeev, Mejo George, Levin John, Athira Perunelly Gopalakrishnan, Pahal Priyanka, Spoorthi Mendon, Tanuja Yandigeri, Mahammad Nisar, Muhammad Nisar, Saptami Kanekar, Rex Devasahayam Arokia Balaya, Rajesh Raju
Homeodomain-interacting protein kinase 1 (HIPK1) is majorly found in the nucleoplasm. HIPK1 is associated with cell proliferation, tumor necrosis factor-mediated cellular apoptosis, transcription regulation, and DNA damage response, and thought to play significant roles in health and common diseases such as cancer. Despite this, HIPK1 remains an understudied molecular target. In the present study, based on a systematic screening and mapping approach, we assembled 424 qualitative and 44 quantitative phosphoproteome datasets with 15 phosphosites in HIPK1 reported across multiple studies...
March 18, 2024: Omics: a Journal of Integrative Biology
https://read.qxmd.com/read/38498010/rna-small-molecule-interaction-challenging-the-undruggable-tag
#2
REVIEW
Jaskirat Kaur, Akanksha Sharma, Poonam Mundlia, Vikas Sood, Ankur Pandey, Gurpal Singh, Ravi Pratap Barnwal
RNA targeting, specifically with small molecules, is a relatively new and rapidly emerging avenue with the promise to expand the target space in the drug discovery field. From being "disregarded" as an "undruggable" messenger molecule to FDA approval of an RNA-targeting small-molecule drug Risdiplam, a radical change in perspective toward RNA has been observed in the past decade. RNAs serve important regulatory functions beyond canonical protein synthesis, and their dysregulation has been reported in many diseases...
March 18, 2024: Journal of Medicinal Chemistry
https://read.qxmd.com/read/38497812/pleiotropic-effects-of-trisomy-and-pharmacologic-modulation-on-structural-functional-molecular-and-genetic-systems-in-a-down-syndrome-mouse-model
#3
JOURNAL ARTICLE
Sergi Llambrich, Birger Tielemans, Ellen Saliën, Marta Atzori, Kaat Wouters, Vicky Van Bulck, Mark Platt, Laure Vanherp, Nuria Gallego Fernandez, Laura Grau de la Fuente, Harish Poptani, Lieve Verlinden, Uwe Himmelreich, Anca Croitor, Catia Attanasio, Zsuzsanna Callaerts-Vegh, Willy Gsell, Neus Martínez-Abadías, Greetje Vande Velde
Down syndrome (DS) is characterized by skeletal and brain structural malformations, cognitive impairment, altered hippocampal metabolite concentration and gene expression imbalance. These alterations were usually investigated separately, and the potential rescuing effects of green tea extracts enriched in epigallocatechin-3-gallate (GTE-EGCG) provided disparate results due to different experimental conditions. We overcame these limitations by conducting the first longitudinal controlled experiment evaluating genotype and GTE-EGCG prenatal chronic treatment effects before and after treatment discontinuation...
March 18, 2024: ELife
https://read.qxmd.com/read/38497789/single-cell-rna-sequencing-unveils-the-hidden-powers-of-zebrafish-kidney-for-generating-both-hematopoiesis-and-adaptive-antiviral-immunity
#4
JOURNAL ARTICLE
Chongbin Hu, Nan Zhang, Yun Hong, Ruxiu Tie, Dongdong Fan, Aifu Lin, Ye Chen, Li-Xin Xiang, Jian-Zhong Shao
The vertebrate kidneys play two evolutionary conserved roles in waste excretion and osmoregulation. Besides, the kidney of fish is considered as a functional ortholog of mammalian bone marrow that serves as a hematopoietic hub for generating blood cell lineages and immunological responses. However, knowledge about the properties of kidney hematopoietic cells, and the functionality of the kidney in fish immune systems remains to be elucidated. To this end, our present study generated a comprehensive atlas with 59 hematopoietic stem/progenitor cell (HSPC) and immune-cells types from zebrafish kidneys via single-cell transcriptome profiling analysis...
March 18, 2024: ELife
https://read.qxmd.com/read/38497758/use-of-rna-biomarkers-in-the-antidoping-field
#5
REVIEW
Francesco Loria, Silke Grabherr, Tiia Kuuranne, Nicolas Leuenberger
There is growing evidence that various RNA molecules can serve as biomarkers for clinical diagnoses. Over the last decade, the high specificities and sensitivities of RNA biomarkers have led to proposals that they could be used to detect prohibited substances and practices in sports. mRNAs and circulating miRNAs have the potential to improve the detection of doping and expand the performance of the Athlete Biological Passport. This review provides a summary of the use of RNA biomarkers to detect human and equine doping practices, including a discussion of the use of dried blood spots as a stable matrix that supports and improves the general process of RNA biomarker detection...
March 18, 2024: Bioanalysis
https://read.qxmd.com/read/38497732/in-situ-visualization-of-rna-specific-sialylation-on-living-cell-membranes-to-explore-n-glycosylation-sites
#6
JOURNAL ARTICLE
Huipu Liu, Xuemei Li, Yi Ren, Yuanjiao Yang, Yunlong Chen, Huangxian Ju
The small RNAs on living cell membranes were recently found to be N -glycosylated and terminated with sialic acids, although the glycosylation sites and potential functions remain unclear. Herein, we designed a second-generation hierarchical coding strategy (HieCo 2) for in situ visualization of cell surface RNA-specific sialylation. After covalently binding DNA codes to sialic acids and then binding a DNA code to a target RNA via sequence specificity, cascade decoding processes were performed with subsequent signal amplification that enabled sensitive in situ visualization of low-abundance Y5 RNA-specific sialic acids on living cell membranes...
March 18, 2024: Journal of the American Chemical Society
https://read.qxmd.com/read/38497483/circalms1-alleviates-pulmonary-microvascular-endothelial-cell-dysfunction-in-pulmonary-hypertension
#7
JOURNAL ARTICLE
Xiaoyi Hu, Yuanyuan Sun, Shang Wang, Hui Zhao, Yaqin Wei, Jiaqi Fu, Yuxia Huang, Wenhui Wu, Jinling Li, Jinming Liu, Sugang Gong, Qinhua Zhao, Lan Wang, Rong Jiang, Xiao Song, Ping Yuan
BACKGROUND: Circular RNAs can serve as regulators influencing the development of pulmonary hypertension (PH). However, their function in pulmonary vascular intimal injury remains undefined. Thus, we aimed to identify specifically expressed circular RNAs in pulmonary microvascular endothelial cells (PMECs) under hypoxia and PH. METHODS AND RESULTS: Deep RNA sequencing and quantitative real-time polymerase chain reaction revealed that circALMS1 (circular RNA Alstrom syndrome protein 1) was reduced in human PMECs under hypoxia ( P <0...
March 18, 2024: Journal of the American Heart Association
https://read.qxmd.com/read/38497076/deciphering-aging-associated-molecular-mechanisms-in-bone-marrow-derived-hematopoietic-stem-cells-in-the-elderly-using-ngs-data
#8
JOURNAL ARTICLE
Hind A Alkhatabi
Aging is a complex process that is not yet fully understood. Despite advancements in research, a deeper understanding of the underlying biological mechanisms is necessary to develop interventions that promote healthy longevity. The aim of this study was to elucidate the complex mechanisms associated with healthy aging and longevity in healthy elderly individuals. The RNA sequencing (RNA-seq) data used in this study was obtained from the Gene Expression Omnibus (GEO) database (accession number GSE104406), which was collected from Fluorescent Activated Cell Sorting (FACS) of human bone marrow derived human hematopoietic stem cells (BM-HSCs) (Lineage-, CD34+, CD38-) young (18-30 years old) and aged (65-75 years old) donors who had no known hematological malignancy, with 10 biological replicates per group...
2024: Bioinformation
https://read.qxmd.com/read/38496838/long-noncoding-rna-linc00858-aggravates-the-progression-of-esophageal-squamous-cell-carcinoma-via-regulating-the-mir-425-5p-abl2-axis
#9
JOURNAL ARTICLE
Pengfei Li, Hui Ding, Shuangyin Han, Songze Ding, Yuxiu Yang
Esophageal squamous cell carcinoma (ESCC) is one of the most fatal cancers with high morbidity and mortality, which severely affects people's lives. Long intergenic non-protein coding RNA 858 (LINC00858) was confirmed to promote the progression of colorectal cancer and lung cancer. However, the role of lncRNA LINC00858 is still unknown in ESCC. Herein, the main purpose of research was to explore LINC00858 function and its impact on ESCC cell biological behaviors. RT-qPCR was used to test the expression of LINC00858, miR-425-5p and ABL proto-oncogene 2 (ABL2) in ESCC cells...
March 30, 2024: Heliyon
https://read.qxmd.com/read/38496620/spatial-visualization-of-a-to-i-editing-in-cells-using-endonuclease-v-immunostaining-assay-endovia
#10
Alexandria L Quillin, Benoît Arnould, Steve D Knutson, Jennifer M Heemstra
Adenosine-to-Inosine (A-to-I) editing is one of the most widespread post-transcriptional RNA modifications and is catalyzed by adenosine deaminases acting on RNA (ADARs). Varying across tissue types, A-to-I editing is essential for numerous biological functions and dysregulation leads to autoimmune and neurological disorders, as well as cancer. Recent evidence has also revealed a link between RNA localization and A-to-I editing, yet understanding of the mechanisms underlying this relationship and its biological impact remains limited...
March 5, 2024: bioRxiv
https://read.qxmd.com/read/38496579/fibroblasts-as-an-in-vitro-model-of-circadian-genetic-and-genomic-studies-a-temporal-analysis
#11
Marcelo Francia, Merel Bot, Toni Boltz, Juan F De la Hoz, Marco Boks, René Kahn, Roel Ophoff
Bipolar disorder (BD) is a heritable disorder characterized by shifts in mood that manifest in manic or depressive episodes. Clinical studies have identified abnormalities of the circadian system in BD patients as a hallmark of underlying pathophysiology. Fibroblasts are a well-established in vitro model for measuring circadian patterns. We set out to examine the underlying genetic architecture of circadian rhythm in fibroblasts, with the goal to assess its contribution to the polygenic nature of BD disease risk...
March 5, 2024: bioRxiv
https://read.qxmd.com/read/38496463/modeling-the-genomic-complexity-of-human-cancer-using-cas12a-mice
#12
Jess D Hebert, Haiqing Xu, Yuning J Tang, Paloma A Ruiz, Colin Detrick, Jing Wang, Nicholas W Hughes, Oscar Donosa, Laura Andrejka, Saswati Karmakar, Irenosen Aboiralor, Le Cong, Julien Sage, Dmitri A Petrov, Monte M Winslow
Somatic genome editing in mouse models has increased our understanding of the in vivo effects of genetic alterations in areas ranging from neuroscience to cancer biology and beyond. However, existing models have been restricted in their ability to create multiple targeted edits, which has limited investigations into complex genetic interactions that underlie development, homeostasis, and disease. To accelerate and expand the generation of complex genotypes in somatic cells, we generated transgenic mice with Cre-regulated and constitutive expression of enhanced Acidaminococcus sp...
March 8, 2024: bioRxiv
https://read.qxmd.com/read/38496012/biological-characteristics-of-muse-cells-derived-from-menscs-and-their-application-in-acute-liver-injury-and-intracerebral-hemorrhage-diseases
#13
JOURNAL ARTICLE
Han Li, Jinghui Wei, Mingzhi Li, Yaoqiang Li, Tong Zhang, Jialu Tian, Xuejia Liu, Kangjia Li, Juntang Lin
The increasing interest in multilineage differentiating stress-enduring (Muse) cells within the field of regenerative medicine is attributed to their exceptional homing capabilities, prolonged viability in adverse conditions, and enhanced three-germ-layer differentiate ability, surpassing their parent mesenchymal stem cells. Given their abundant sources, non-invasive collection procedure, and periodic availability, human menstrual blood-derived endometrium stem cells (MenSCs) have been extensively investigated as a potential resource for stem cell-based therapies...
December 2024: Regenerative Therapy
https://read.qxmd.com/read/38495916/from-static-to-dynamic-the-influence-of-mechanotransduction-on-skin-equivalents-analyzed-by-bioimaging-and-rnaseq
#14
JOURNAL ARTICLE
Katharina Kaiser, Sofie M Bendixen, Jens Ahm Sørensen, Jonathan R Brewer
In this study, we explore the impact of mechanical stimuli on skin models using an innovative skin-on-a-chip platform, addressing the limitations of conventional transwell-cultured skin equivalents. This platform facilitates cyclic mechanical stimulation through compression and stretching, combined with automated media perfusion. Our findings, using bioimaging and bulk RNA sequencing, reveal increased expression of Keratin 10 and Keratin 14, indicating enhanced skin differentiation and mechanical integrity...
April 2024: Materials today. Bio
https://read.qxmd.com/read/38495876/leukemic-mutation-flt3-itd-is-retained-in-dendritic-cells-and-disrupts-their-homeostasis-leading-to-expanded-th17-frequency
#15
JOURNAL ARTICLE
Patrick A Flynn, Mark D Long, Yoko Kosaka, Nicola Long, Jessica S Mulkey, Jesse L Coy, Anupriya Agarwal, Evan F Lind
Dendritic cells (DC) are mediators between innate and adaptive immune responses to pathogens and tumors. DC development is determined by signaling through the receptor tyrosine kinase Fms-like tyrosine kinase 3 (FLT3) in bone marrow myeloid progenitors. Recently the naming conventions for DC phenotypes have been updated to distinguish between "Conventional" DCs (cDCs) and plasmacytoid DCs (pDCs). Activating mutations of FLT3, including Internal Tandem Duplication (FLT3-ITD), are associated with poor prognosis for acute myeloid leukemia (AML) patients...
2024: Frontiers in Immunology
https://read.qxmd.com/read/38495845/modifying-mirs-for-effective-reprogramming-of-fibroblasts-to-cardiomyocytes
#16
JOURNAL ARTICLE
Xinghua Wang, Syeda S Baksh, Richard E Pratt, Victor J Dzau, Conrad P Hodgkinson
Reprogramming scar fibroblasts into cardiomyocytes has been proposed to reverse the damage associated with myocardial infarction. However, the limited improvement in cardiac function calls for enhanced strategies. We reported enhanced efficacy of our miR reprogramming cocktail miR combo (miR-1, miR-133a, miR-208a, and miR-499) via RNA-sensing receptor stimulation. We hypothesized that we could combine RNA-sensing receptor activation with fibroblast reprogramming by chemically modifying miR combo. To test the hypothesis, miR combo was modified to enhance interaction with the RNA-sensing receptor Rig1 via the addition of a 5'-triphosphate (5'ppp) group...
June 11, 2024: Molecular Therapy. Nucleic Acids
https://read.qxmd.com/read/38495844/metabolism-pathway-based-subtyping-in-endometrial-cancer-an-integrated-study-by%C3%A2-multi-omics-analysis-and-machine-learning-algorithms
#17
JOURNAL ARTICLE
Xiaodie Liu, Wenhui Wang, Xiaolei Zhang, Jing Liang, Dingqing Feng, Yuebo Li, Ming Xue, Bin Ling
Endometrial cancer (EC), the second most common malignancy in the female reproductive system, has garnered increasing attention for its genomic heterogeneity, but understanding of its metabolic characteristics is still poor. We explored metabolic dysfunctions in EC through a comprehensive multi-omics analysis (RNA-seq datasets from The Cancer Genome Atlas [TCGA], Cancer Cell Line Encyclopedia [CCLE], and GEO datasets; the Clinical Proteomic Tumor Analysis Consortium [CPTAC] proteomics; CCLE metabolomics) to develop useful molecular targets for precision therapy...
June 11, 2024: Molecular Therapy. Nucleic Acids
https://read.qxmd.com/read/38495826/transcriptome-regulation-by-parp13-in-basal-and-antiviral-states-in-human-cells
#18
JOURNAL ARTICLE
Veronica F Busa, Yoshinari Ando, Stefan Aigner, Brian A Yee, Gene W Yeo, Anthony K L Leung
The RNA-binding protein PARP13 is a primary factor in the innate antiviral response, which suppresses translation and drives decay of bound viral and host RNA. PARP13 interacts with many proteins encoded by interferon-stimulated genes (ISG) to activate antiviral pathways including co-translational addition of ISG15, or ISGylation. We performed enhanced crosslinking immunoprecipitation (eCLIP) and RNA-seq in human cells to investigate PARP13's role in transcriptome regulation for both basal and antiviral states...
April 19, 2024: IScience
https://read.qxmd.com/read/38495671/genome-wide-identification-of-dysregulated-alternative-splicing-and-rna-binding-proteins-involved-in-atopic-dermatitis
#19
JOURNAL ARTICLE
Yaqi Yang, Hao Chen, Qing Jiang, Lin Yang, Rongfei Zhu, Nan Huang
Objectives: We explored the role and molecular mechanisms of RNA-binding proteins (RBPs) and their regulated alternative splicing events (RASEs) in the pathogenesis of atopic dermatitis (AD). Methods: We downloaded RNA-seq data (GSE121212) from 10 healthy control skin samples (healthy, Ctrl), 10 non-lesional skin samples with AD damage (non-lesional, NL), and 10 lesional skin samples with AD damage (lesional, LS). We performed the analysis of differentially expressed genes (DEGs), differentially expressed RBPs (DE-RBPs), alternative splicing (AS), functional enrichment, the co-expression of RBPs and RASEs, and quantitative polymerase chain reaction (qPCR)...
2024: Frontiers in Genetics
https://read.qxmd.com/read/38495587/the-regulation-of-triglyceride-and-glycogen-storage-by-glucose-transporter-1-glut1-in-drosophila-fat-tissue
#20
JOURNAL ARTICLE
Louis S Betz, Justin R DiAngelo
Obesity reflects an imbalance in nutrient storage resulting in excess fat accumulation. The molecules that tissues use to regulate nutrient storage are not well understood. A previously published genetic screen using Drosophila melanogaster larvae identified Glut1 , a transmembrane glucose transporter, as a potential obesity gene. To identify the adipose-specific functions of this gene, Glut1 levels were decreased using RNAi targeted to fly fat tissue. Adult Glut1 RNAi flies have lower glycogen and triglyceride levels, as well as decreased FASN1 RNA expression...
2024: microPublication. Biology
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