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JOURNAL ARTICLE
Aline Martin, Riki Kawaguchi, Qing Wang, Isidro B Salusky, Renata C Pereira, Katherine Wesseling-Perry
Maturation defects are intrinsic features of osteoblast lineage cells in CKD patients. These defects persist ex vivo, suggesting that CKD induces epigenetic changes in bone cells. To gain insights into which signaling pathways contribute to CKD-mediated, epigenetically driven, impairments in osteoblast maturation, we characterized RNA expression and DNA methylation patterns by RNA-Seq and MethylationEpic in primary osteoblasts from nine adolescent and young adult dialysis patients with end-stage kidney disease and three healthy references...
January 2024: JBMR Plus
#2
JOURNAL ARTICLE
Marco Palmesano, Andrea Lisa, Gabriele Storti, Manuela Bottoni, Alessandra Gottardi, Giulia Colombo, Benedetta Barbieri, Cristina Garusi, Pietro Sala, Giorgio Lo Iacono, Lorenzo Spaggiari, Francesca De Lorenzi, Valerio Cervelli, Mario Rietjens
BACKGROUND: Chest-wall sarcomas are treated with extensive resections and complex defect reconstruction to restore chest-wall integrity. It is a difficult surgical procedure that incorporates a multidisciplinary approach for the best outcome, preventing paradoxical chest movement issues and reducing complications. OBJECTIVE: We aimed to describe our experience of chest-wall reconstruction using polypropylene mesh (Marlex® Mesh) combined with methyl-methacrylate and soft-tissue coverage with a latissimus dorsi flap following sarcoma resection...
April 15, 2024: Journal of Plastic, Reconstructive & Aesthetic Surgery: JPRAS
#3
JOURNAL ARTICLE
Bin Chen, Yi Liu, Yuping He, Chenfu Shen
BACKGROUND: Interleukin-4 inducible gene 1 (IL4I1) regulates tumor progression in numerous tumor types. However, its correlation with immune infiltration and prognosis of patients in a pan-cancer setting remains unclear. METHODS: Data from the Cancer Genome Atlas (TCGA), Genotype-Tissue Expression (GTEx), UALCAN, Clinical Proteomic Tumor Analysis Consortium (CPTAC), Gene Expression Omnibus (GEO), cBioPortal, Cancer Single-cell State Atlas (CancerSEA), and Tumor IMmune Estimation Resource(TIMER) databases were used to evaluate IL4I1 expression, clinical features and prognostic effects, gene set enrichment, and correlation with immune cell infiltration, as well as the relationship between IL4I1 methylation and expression and survival prognosis...
May 1, 2024: Discover. Oncology
#4
JOURNAL ARTICLE
Mingqi Zhou, Alberto Riva, Marie-Pierre L Gauthier, Michael P Kladde, Robert J Ferl, Anna-Lisa Paul
BACKGROUND: The Advanced Plant Experiment-04 - Epigenetic Expression (APEX-04-EpEx) experiment onboard the International Space Station examined the spaceflight-altered cytosine methylation in two genetic lines of Arabidopsis thaliana, wild-type Col-0 and the mutant elp2-5, which is deficient in an epigenetic regulator Elongator Complex Subunit 2 (ELP2). Whole-genome bisulfite sequencing (WGBS) revealed distinct spaceflight associated methylation differences, presenting the need to explore specific space-altered methylation at single-molecule resolution to associate specific changes over large regions of spaceflight related genes...
April 30, 2024: Biology Direct
#5
JOURNAL ARTICLE
Min Kyung Lee, Nasim Azizgolshani, Ze Zhang, Laurent Perreard, Fred W Kolling, Lananh N Nguyen, George J Zanazzi, Lucas A Salas, Brock C Christensen
Although intratumoral heterogeneity has been established in pediatric central nervous system tumors, epigenomic alterations at the cell type level have largely remained unresolved. To identify cell type-specific alterations to cytosine modifications in pediatric central nervous system tumors, we utilize a multi-omic approach that integrated bulk DNA cytosine modification data (methylation and hydroxymethylation) with both bulk and single-cell RNA-sequencing data. We demonstrate a large reduction in the scope of significantly differentially modified cytosines in tumors when accounting for tumor cell type composition...
April 30, 2024: Nature Communications
#6
JOURNAL ARTICLE
Daniela Cesana, Maria Pia Cicalese, Andrea Calabria, Pietro Merli, Roberta Caruso, Monica Volpin, Laura Rudilosso, Maddalena Migliavacca, Federica Barzaghi, Claudia Fossati, Francesco Gazzo, Simone Pizzi, Andrea Ciolfi, Alessandro Bruselles, Francesca Tucci, Giulio Spinozzi, Giulia Pais, Fabrizio Benedicenti, Matteo Barcella, Ivan Merelli, Pierangela Gallina, Stefania Giannelli, Francesca Dionisio, Serena Scala, Miriam Casiraghi, Luisa Strocchio, Luciana Vinti, Lucia Pacillo, Eleonora Draghi, Marcella Cesana, Sara Riccardo, Chiara Colantuono, Emmanuelle Six, Marina Cavazzana, Filippo Carlucci, Manfred Schmidt, Caterina Cancrini, Fabio Ciceri, Luca Vago, Davide Cacchiarelli, Bernhard Gentner, Luigi Naldini, Marco Tartaglia, Eugenio Montini, Franco Locatelli, Alessandro Aiuti
Hematopoietic stem cell gene therapy (GT) using a γ-retroviral vector (γ-RV) is an effective treatment for Severe Combined Immunodeficiency due to Adenosine Deaminase deficiency. Here, we describe a case of GT-related T-cell acute lymphoblastic leukemia (T-ALL) that developed 4.7 years after treatment. The patient underwent chemotherapy and haploidentical transplantation and is currently in remission. Blast cells contain a single vector insertion activating the LIM-only protein 2 (LMO2) proto-oncogene, confirmed by physical interaction, and low Adenosine Deaminase (ADA) activity resulting from methylation of viral promoter...
April 30, 2024: Nature Communications
#7
JOURNAL ARTICLE
Junming Qian, Shawn X Liu
DNA methylation is a key epigenetic mechanism underlying many biological processes, and its aberrant regulation has been tightly associated with various human diseases. Precise manipulation of DNA methylation holds the promise to advance our understanding of this critical mechanism and to develop novel therapeutic methods. Previously, we were only able to alter genome-wide DNA methylation by treating with small molecules (e.g., 5-Aza-2-deoxycytidine) or perturbing relevant genes (e.g., DNA methyltransferase) targetlessly, which makes it challenging to investigate the functional significance of this epigenetic mark at specific genomic loci...
April 20, 2024: Bio-protocol
#8
JOURNAL ARTICLE
Nissi Sharon, Vinod G Ugale, Pannala Padmaja, Deepak Lokwani, Chandradeep Salunkhe, Padmaja Shete, Pedavenkatagari Narayana Reddy, Prasad P Kulkarni
Alzheimer's disease (AD) is a neurodegenerative disease affecting mental ability and neurocognitive functions. Cholinesterase enzymes affect concentration of acetylcholine in the brain, leading to dementia. Thus, there is an urgent need to develop novel dual cholinesterase inhibitors as possible anti-AD drugs. Herein, we have designed and synthesized a novel series of 9H-carbazole-4H-chromenes 4(a-l) through a one-pot three-component reaction of salicylaldehydes (1), hydroxycarbazole (2) and N-methyl-1-(methylthio)-2-nitroethenamine (3) using triethylamine as a catalyst in ethanol...
April 29, 2024: Molecular Diversity
#9
JOURNAL ARTICLE
Yang Lin, Chang-Hyun Gil, Kimihiko Banno, Masataka Yokoyama, Matthew Wingo, Ellen Go, Nutan Prasain, Ying Liu, Takashi Hato, Hisamichi Naito, Taku Wakabayashi, Musia Sominskaia, Meng Gao, Kevin Chen, Fuqiang Geng, Jesus Maria Gomez Salinero, Sisi Chen, W Christopher Shelley, Momoko Yoshimoto, Sergio Li Calzi, Michael P Murphy, Kyoji Horie, Maria B Grant, Ryan Schreiner, David Redmond, David P Basile, Shahin Rafii, Mervin C Yoder
BACKGROUND: Most organs are maintained lifelong by resident stem/progenitor cells. During development and regeneration, lineage-specific stem/progenitor cells can contribute to the growth or maintenance of different organs, whereas fully differentiated mature cells have less regenerative potential. However, it is unclear whether vascular endothelial cells (ECs) are also replenished by stem/progenitor cells with EC-repopulating potential residing in blood vessels. It has been reported recently that some EC populations possess higher clonal proliferative potential and vessel-forming capacity compared with mature ECs...
April 29, 2024: Circulation
#10
JOURNAL ARTICLE
Achara Raksat, Md Samiul Huq Atanu, Sheyanne Mendez, Rafael de la Zerda, Rui Sun, Sarot Cheenpracha, Marisa Wall, Charles J Simmons, Philip G Williams, Ghee T Tan, Supakit Wongwiwatthananukit, Leng Chee Chang
The fruit extract of Melaleuca quinquenervia yielded a total of 19 compounds, including two novel spiro-biflavonoid enantiomers ( 1a and 1b ) and a chalcone derivative ( 3 ). Their structures were determined through spectroscopic analysis. The enantiomers of the racemic mixture of compound 1 were successfully resolved into (+)- 1 and (-)- 1 using chiral-phase HPLC. Single-crystal X-ray diffraction analysis was also used to confirm the structure of 1 . The enantiomeric configurations of 1 and 2 were determined through a comparison of the calculated and experimental electronic circular dichroism spectra...
April 23, 2024: ACS Omega
#11
JOURNAL ARTICLE
Zihui Yu, Ziying Xu, Shang Li, Ziyan Tian, Jing Yuan
A growing number of studies suggest a positive association between obesity and the high incidence of papillary thyroid cancer (PTC), suggesting that the abnormal levels of adipokines associated with obesity may be a risk factor for these aggressive thyroid cancers, but the underlying regulatory mechanisms are not yet clear. We downloaded bulk RNA sequence data for subcutaneous adipose tissue (SAT) in obesity and healthy population and tumor tissues of PTC from GEO database. Through analysis of Differential Expression Genes (DEGs), Gene Set Variation Analysis (GSVA) and Weighted Correlation Network Analysis (WGCNA), we identified co-expressed genes between obesity and PTC, and their pathways were mainly enriched in the regulation of B-cells...
April 28, 2024: Cellular and Molecular Biology
#12
JOURNAL ARTICLE
Basile Leduque, Alejandro Edera, Clémentine Vitte, Leandro Quadrana
Epigenetic regulations, including chromatin accessibility, nucleosome positioning and DNA methylation intricately shape genome function. However, current chromatin profiling techniques relying on short-read sequencing technologies fail to characterise highly repetitive genomic regions and cannot detect multiple chromatin features simultaneously. Here, we performed Simultaneous Accessibility and DNA Methylation Sequencing (SAM-seq) of purified plant nuclei. Thanks to the use of long-read nanopore sequencing, SAM-seq enables high-resolution profiling of m6A-tagged chromatin accessibility together with endogenous cytosine methylation in plants...
April 27, 2024: Nucleic Acids Research
#13
REVIEW
Iacopo Passeri, Francesca Vaccaro, Alessio Mengoni, Camilla Fagorzi
The universality of DNA methylation as an epigenetic regulatory mechanism belongs to all biological kingdoms. However, while eukaryotic systems have been the primary focus of DNA methylation studies, the molecular mechanisms in prokaryotes are less known. Nevertheless, DNA methylation in prokaryotes plays a pivotal role in many cellular processes such as defense systems against exogenous DNA, cell cycle dynamics, and gene expression, including virulence. Thanks to single-molecule DNA sequencing technologies, genome-wide identification of methylated DNA is becoming feasible on a large scale, providing the possibility to investigate more deeply the presence, variability, and roles of DNA methylation...
April 17, 2024: International Journal of Molecular Sciences
#14
JOURNAL ARTICLE
Jiaojiao Niu, Yeng Chen, Hwa Chia Chai, Sreenivasan Sasidharan
BACKGROUND: MiR-484, implicated in various carcinomas, holds promise as a prognostic marker, yet its relevance to cervical cancer (CC) remains unclear. Our prior study demonstrated the Polyalthia longifolia downregulation of miR-484, inhibiting HeLa cells. This study investigates miR-484's potential as a biomarker and therapeutic target in CC through integrated bioinformatics and an in vitro analysis. METHODS: MiR-484 levels were analyzed across cancers, including CC, from The Cancer Genome Atlas...
April 19, 2024: Biomedicines
#15
JOURNAL ARTICLE
Alex Chialastri, Saumya Sarkar, Elizabeth E Schauer, Shyl Lamba, Siddharth S Dey
Inheritance of 5-methylcytosine from one cell generation to the next by DNA methyltransferase 1 (DNMT1) plays a key role in regulating cellular identity. While recent work has shown that the activity of DNMT1 is imprecise, it remains unclear how the fidelity of DNMT1 is tuned in different genomic and cell state contexts. Here we describe Dyad-seq, a method to quantify the genome-wide methylation status of cytosines at the resolution of individual CpG dinucleotides to find that the fidelity of DNMT1-mediated maintenance methylation is related to the local density of DNA methylation and the landscape of histone modifications...
April 26, 2024: Nature Structural & Molecular Biology
#16
JOURNAL ARTICLE
Jianjin Wu, Lei Wang, Shuaishuai Xi, Chao Ma, Fukang Zou, Guanyu Fang, Fangbing Liu, Xiaokai Wang, Lefeng Qu
BACKGROUND: N6-methyladenosine (m6A) methylation is involved in the pathogenesis of atherosclerosis (AS). Limited studies have examined the role of the m6A methyltransferase METTL5 in AS pathogenesis. METHODS: This study subjected the AS dataset to differential analysis and weighted gene co-expression network analysis to identify m6A methylation-associated differentially expressed genes (DEGs). Next, the m6A methylation-related DEGs were subjected to consensus clustering to categorize AS samples into distinct m6A subtypes...
April 24, 2024: Aging
#17
JOURNAL ARTICLE
Zeinab Abdelrahman, Alaa Abdelatty, Jiangti Luo, Amy Jayne McKnight, Xiaosheng Wang
BACKGROUND: Brain tumours are known to have a high mortality and morbidity rate due to their localised and frequent invasive growth. The concept that glioma resistance could originate from the dissimilarity in the vulnerability of clonogenic glial stem cells to chemotherapeutic drugs and radiation has driven the scientific community to reexamine the comprehension of glioma growth and strategies that target these cells or modify their stemness. METHODS: Based on the enrichment scores of 12 stemness signatures, we identified glioma subtypes in both tumour bulks and single cells by clustering analysis...
March 22, 2024: Computers in Biology and Medicine
#18
JOURNAL ARTICLE
Marijana P Kasalović, Sanja Jelača, Žiko Milanović, Danijela Maksimović-Ivanić, Sanja Mijatović, Jelena Lađarević, Bojan Božić, Zoran Marković, Duško Dunđerović, Tobias Rüffer, Robert Kretschmer, Goran N Kaluđerović, Nebojša Đ Pantelić
Three newly synthesized triphenyltin(IV) compounds, Ph3SnL1 (L1- = 3-(4-methyl-2-oxoquinolin-1(2 H )-yl)propanoato), Ph3SnL2 (L2- = 2-(4-methyl-2-oxoquinolin-1(2 H )-yl)ethanoato), and Ph3SnL3 (L3- = 2-(4-hydroxy-2-oxoquinolin-1(2 H )-yl)ethanoato), were characterized by elemental microanalysis, FT-IR spectroscopy and multinuclear (1 H, 13 C and 119 Sn) NMR spectroscopy. A single X-ray diffraction study indicates that compounds Ph3SnL1 and Ph3SnL2 exhibit a 1D zig-zag chain polymeric structure, which in the case of Ph3SnL2 is additionally stabilized by π-interactions...
April 25, 2024: Dalton Transactions: An International Journal of Inorganic Chemistry
#19
JOURNAL ARTICLE
Yong Pan, Yi-Ru Zhang, Ling-Yun Wang, Li-Na Wu, Ying-Qiu Ma, Zhou Fang, Shi-Bo Li
BACKGROUND: Competitive endogenous RNA (ceRNA) is an innovative way of gene expression modulation, which plays a crucial part in neoplasia. However, the intricacy and behavioral characteristics of the ceRNA network in hepatocellular carcinoma (HCC) remain dismal. AIM: To establish a cyclin dependent kinase inhibitor 2A (CDKN2A)-related ceRNA network and recognize potential prognostic indicators for HCC. METHODS: The mutation landscape of CDKN2A in HCC was first explored using the cBioPortal database...
April 15, 2024: World Journal of Gastrointestinal Oncology
#20
JOURNAL ARTICLE
Pierre Romero, Laia Richart, Setareh Aflaki, Ambre Petitalot, Megan Burton, Audrey Michaud, Julien Masliah-Planchon, Frédérique Kuhnowski, Samuel Le Cam, Carlos Baliñas-Gavira, Céline Méaudre, Armelle Luscan, Abderaouf Hamza, Patricia Legoix, Anne Vincent-Salomon, Michel Wassef, Daniel Holoch, Raphaël Margueron
Mutations in chromatin regulators are widespread in cancer. Among them, the histone H3 lysine 27 methyltransferase Polycomb Repressive Complex 2 (PRC2) shows distinct alterations according to tumor type. This specificity is poorly understood. Here, we model several PRC2 alterations in one isogenic system to reveal their comparative effects. Focusing then on lymphoma-associated EZH2 mutations, we show that Ezh2Y641F induces aberrant H3K27 methylation patterns even without wild-type Ezh2, which are alleviated by partial PRC2 inhibition...
April 24, 2024: Nature Communications
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