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REVIEW
Dana-Mihaela Asiminicesei, Daniela Ionela Fertu, Maria Gavrilescu
The paper provides a comprehensive examination of heavy metal stress on medicinal plants, focusing on its impact on antioxidant capacity and biosynthetic pathways critical to their therapeutic potential. It explores the complex relationship between heavy metals and the physiological and biochemical responses of medicinal plants, highlighting how metal stress disrupts biosynthetic pathways, altering concentrations of secondary metabolites. This disruption may compromise the overall quality and efficacy of medicinal plants, requiring a holistic understanding of its cumulative impacts...
March 21, 2024: Plants (Basel, Switzerland)
#22
JOURNAL ARTICLE
Araceli Valverde, Raza Ali Naqvi, Afsar R Naqvi
INTRODUCTION: Macrophages (Mφs) are functionally dynamic immune cells that bridge innate and adaptive immune responses; however, the underlying epigenetic mechanisms that control Mφ plasticity and innate immune functions are not well elucidated. OBJECTIVE: To identify novel functions of macrophage-enriched lncRNAs in regulating polarization and innate immune responses. METHODS: Total RNA isolated from differentiating monocyte-derived M1 and M2 Mφs was profiled for lncRNAs expression using RNAseq...
April 9, 2024: Inflammation Research: Official Journal of the European Histamine Research Society ... [et Al.]
#23
JOURNAL ARTICLE
Georgia da Silva Feltran, Amanda Fantini de Andrade, Célio Jr da C Fernandes, Rodrigo A Foganholi da Silva, Willian F Zambuzzi
During the morphological changes occurring in osteoblast differentiation, Sonic hedgehog (Shh) plays a crucial role. While some progress has been made in understanding this process, the epigenetic mechanisms governing the expression of Hh signaling members in response to bone morphogenetic protein 7 (BMP7) signaling in osteoblasts remain poorly understood. To delve deeper into this issue, we treated pre-osteoblasts (pObs) with 100 ng/mL of BMP7 for up to 21 days. Initially, we validated the osteogenic phenotype by confirming elevated expression of well-defined gene biomarkers, including Runx2, Osterix, Alkaline Phosphatase (Alp), and bone sialoprotein (Bsp)...
April 9, 2024: Cell Biology International
#24
JOURNAL ARTICLE
Yiyang Wang, Yongxiang Li, Yubo Jing, Yuqi Yang, Haiyan Wang, Dilimulati Ismtula, Chenming Guo
The α-tubulin subtype, Tubulin α-1b chain (TUBA1B), has been shown to influence immune cell infiltration, cancer growth, and survival across various malignancies. However, a comprehensive study has not yet been undertaken examining the immunological and predictive effects of TUBA1B in a pan-carcinoma context. Using data from TCGA, GEO, and other databases, we analyzed TUBA1B expression across various carcinoma types using transcriptional profiling, prognostic implications, genetic and epigenetic alterations, methylation patterns, and immunological significance...
April 8, 2024: Scientific Reports
#25
JOURNAL ARTICLE
Liuyang Cai, Hengyan Zhu, Qianqian Mou, Po Yee Wong, Linlin Lan, Cherrie W K Ng, Pu Lei, Man Kit Cheung, Daijuanru Wang, Eddy W Y Wong, Eric H L Lau, Zenon W C Yeung, Ronald Lai, Katie Meehan, Sherwood Fung, Kwan Chee A Chan, Vivian W Y Lui, Alfred S L Cheng, Jun Yu, Paul K S Chan, Jason Y K Chan, Zigui Chen
Dysbiosis of the human oral microbiota has been reported to be associated with oral cavity squamous cell carcinoma (OSCC) while the host-microbiota interactions with respect to the potential impact of pathogenic bacteria on host genomic and epigenomic abnormalities remain poorly studied. In this study, the mucosal bacterial community, host genome-wide transcriptome and DNA CpG methylation were simultaneously profiled in tumors and their adjacent normal tissues of OSCC patients. Significant enrichment in the relative abundance of seven bacteria species (Fusobacterium nucleatum, Treponema medium, Peptostreptococcus stomatis, Gemella morbillorum, Catonella morbi, Peptoanaerobacter yurli and Peptococcus simiae) were observed in OSCC tumor microenvironment...
April 8, 2024: NPJ Biofilms and Microbiomes
#26
JOURNAL ARTICLE
Jianlin Wang, Huiwen Ren, Chao Xu, Bo Yu, Yiling Cai, Jian Wang, Xinye Ni
N6-methyladenosine (m6A) and 5-methylcytosine (m5C) RNA modifications have garnered significant attention in the field of epigenetic research due to their close association with human cancers. This study we focus on elucidating the expression patterns of m6A/m5C-related long non-coding RNAs (lncRNAs) in esophageal squamous cell carcinoma (ESCC) and assessing their prognostic significance and therapeutic potential. Transcriptomic profiles of ESCC were derived from public resources. m6A/m5C-related lncRNAs were obtained from TCGA using Spearman's correlations analysis...
April 8, 2024: Scientific Reports
#27
JOURNAL ARTICLE
Tal Falick Michaeli, Ofra Sabag, Batia Azria, Rimma Fok, Nathalie Abudi, Rinat Abramovitch, Jonathan Monin, Yuval Gielchinsky, Howard Cedar, Yehudit Bergman
As a result of partial hepatectomy, the remaining liver tissue undergoes a process of renewed proliferation that leads to rapid regeneration of the liver. By following the early stages of this process, we observed dramatic programmed changes in the DNA methylation profile, characterized by both de novo and demethylation events, with a subsequent return to the original adult pattern as the liver matures. Strikingly, these transient alterations partially mimic the DNA methylation state of embryonic hepatoblasts (E16...
April 16, 2024: Proceedings of the National Academy of Sciences of the United States of America
#28
JOURNAL ARTICLE
Sean Murphy, Sharif Rahmy, Dailin Gan, Guoqiang Liu, Yini Zhu, Maxim Manyak, Loan Duong, Jianping He, James H Schofield, Zachary T Schafer, Jun Li, Xuemin Lu, Xin Lu
Resistance to immune checkpoint blockade (ICB) therapy represents a formidable clinical challenge limiting the efficacy of immunotherapy. In particular, prostate cancer (PCa) poses a challenge for ICB therapy due to its immunosuppressive features. A ketogenic diet (KD) has been reported to enhance response to ICB therapy in some other cancer models. However, adverse effects associated with continuous KD were also observed, demanding better mechanistic understanding and optimized regimens for using KD as an immunotherapy sensitizer...
April 8, 2024: Cancer Research
#29
Ashok Daniel Prabakaran, Hyun-Jy Chung, Kevin McFarland, Thirupugal Govindarajan, Fadoua El Abdellaoui Soussi, Hima Bindu Durumutla, Chiara Villa, Kevin Piczer, Hannah Latimer, Cole Werbrich, Olukunle Akinborewa, Robert Horning, Mattia Quattrocelli
Genetic variations in the glucocorticoid receptor (GR) gene NR3C1 can impact metabolism. The single nucleotide polymorphism (SNP) rs6190 (p.R23K) has been associated in humans with enhanced metabolic health, but the SNP mechanism of action remains completely unknown. We generated a transgenic knock-in mice genocopying this polymorphism to elucidate how the mutant GR impacts metabolism. Compared to non-mutant littermates, mutant mice showed increased muscle insulin sensitivity and strength on regular chow and high-fat diet, blunting the diet-induced adverse effects on weight gain and exercise intolerance...
March 31, 2024: bioRxiv
#30
Vasiliki Leventaki, Timothy Shaw, Stanley Pounds, Xueyuan Cao, Jing Ma, Gustavo Palacios, John Mason, Sherrie Perkins, Gang Wu, Yiping Fan, Jian Wang, Xin Zhou, Alyssa Obermayer, Marsha Kinney, Jacqueline Kraveka, Thomas Gross, John Sandlund, Jinghui Zhang, Charles Mullighan, Megan Lim
Anaplastic large cell lymphoma (ALCL) is a mature T-cell lymphoma that accounts for for 10-15% of childhood lymphomas. Despite the observation that more than 90% of pediatric cases harbor the anaplastic lymphoma kinase (ALK) rearrangement resulting in aberrant ALK kinase expression, there is significant clinical, morphologic, and biological heterogeneity. To gain insights into the genomic aberrations and molecular heterogeneity within ALK-positive ALCL(ALK+ ALCL), we analyzed 46 pediatric ALK+ ALCLs by whole-exome sequencing, RNA-sequencing, and DNA methylation profiling...
March 28, 2024: Research Square
#31
JOURNAL ARTICLE
Nour El Osmani, Corinne Prévostel, Laurence Picque Lasorsa, Mohammad El Harakeh, Zeina Radwan, Hiba Mawlawi, Marwan El Sabban, Margret Shirinian, Zeina Dassouki
Deregulation of ten-eleven Translocation protein 1 (TET1) is commonly reported to induce imbalances in gene expression and subsequently to colorectal cancer development (CRC). On the other hand, vitamin C (VitC) improves the prognosis of colorectal cancer by reprogramming the cancer epigenome and limiting chemotherapeutic drug resistance events. In this study, we aimed to characterize TET1-specific subcellular compartments and evaluate the effect of VitC on TET1 compartmentalization in colonic tumour cells...
December 2024: Epigenetics: Official Journal of the DNA Methylation Society
#32
JOURNAL ARTICLE
Mohamed H Elsafi Mabrouk, Kira Zeevaert, Ann-Christine Henneke, Catharina Maaßen, Wolfgang Wagner
BACKGROUND AIMS: Substrate elasticity may direct cell-fate decisions of stem cells. However, it is largely unclear how matrix stiffness affects the differentiation of induced pluripotent stem cells (iPSCs) and whether this is also reflected by epigenetic modifications. METHODS: We cultured iPSCs on tissue culture plastic (TCP) and polydimethylsiloxane (PDMS) with different Young's modulus (0.2 kPa, 16 kPa or 64 kPa) to investigate the sequel on growth and differentiation toward endoderm, mesoderm and ectoderm...
March 30, 2024: Cytotherapy
#33
JOURNAL ARTICLE
Farshad Nassiri, Andrew Ajisebutu, Vikas Patil, Yasin Mamatjan, Jeff Liu, Justin Z Wang, Mathew R Voisin, Romina Nejad, Sheila Mansouri, Shirin Karimi, Ankur Chakravarthy, Eric Chen, Daniel D De Carvalho, Kenneth Aldape, Gelareh Zadeh
Mutations in the pivotal metabolic isocitrate dehydrogenase (IDH) enzymes are recognized to drive the molecular footprint of diffuse gliomas, and patients with IDH mutant gliomas have overall favorable outcomes compared to patients with IDH wild-type tumors. However, survival still varies widely among patients with IDH mutated tumors. Here, we aimed to characterize molecular signatures that explain the range of IDH mutant gliomas. By integrating matched epigenome-wide methylome, transcriptome, and global metabolome data in 154 patients with gliomas, we identified a group of IDH mutant gliomas with globally altered metabolism that resembled IDH wild-type tumors...
April 7, 2024: Acta Neuropathologica
#34
REVIEW
Taeyoung Ahn, Eun-Ah Bae, Hyungseok Seo
T cell exhaustion, which is observed in various chronic infections and malignancies, is characterized by elevated expression of multiple inhibitory receptors, impaired effector functions, decreased proliferation, and reduced cytokine production. Notably, while adoptive T cell therapies, such as chimeric antigen receptor (CAR)-T therapy, have shown promise in treating cancer and other diseases, the efficacy of these therapies is often compromised by T cell exhaustion. It is imperative, therefore, to understand the mechanisms underlying this exhaustion to promote advances in T cell-related therapies...
April 5, 2024: Molecular Therapy
#35
JOURNAL ARTICLE
Wenqing Zhang, Long Zhang, Yuxin Feng, Dawei Lin, Zhi Yang, Zhifeng Zhang, Yubin Ma
Sulfide is a well-known environmental pollutant that can have detrimental effects on most organisms. However, few metazoans living in sulfide-rich environments have developed mechanisms to tolerate and adapt to sulfide stress. Epigenetic mechanisms, including DNA methylation, have been shown to play a vital role in environmental stress adaptation. Nevertheless, the precise function of DNA methylation in biological sulfide adaptation remains unclear. Urechis unicinctus, a benthic organism inhabiting sulfide-rich intertidal environments, is an ideal model organism for studying adaptation to sulfide environments...
April 4, 2024: Science of the Total Environment
#36
JOURNAL ARTICLE
Yu Xiao, Wan Jin, Kaiyu Qian, Lingao Ju, Gang Wang, Kai Wu, Rui Cao, Luyuan Chang, Zilin Xu, Jun Luo, Liuying Shan, Fang Yu, Xintong Chen, Dongmei Liu, Hong Cao, Yejinpeng Wang, Xinyue Cao, Wei Zhou, Diansheng Cui, Ye Tian, Chundong Ji, Yongwen Luo, Xin Hong, Fangjin Chen, Minsheng Peng, Yi Zhang, Xinghuan Wang
Intratumor heterogeneity (ITH) of bladder cancer (BLCA) contributes to therapy resistance and immune evasion affecting clinical prognosis. The molecular and cellular mechanisms contributing to BLCA ITH generation remain elusive. It is found that a TM4SF1-positive cancer subpopulation (TPCS) can generate ITH in BLCA, evidenced by integrative single cell atlas analysis. Extensive profiling of the epigenome and transcriptome of all stages of BLCA revealed their evolutionary trajectories. Distinct ancestor cells gave rise to low-grade noninvasive and high-grade invasive BLCA...
April 6, 2024: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
#37
JOURNAL ARTICLE
Yu Wei Zhang, Ana Gvozdenovic, Nicola Aceto
UNLABELLED: Circulating tumor cells (CTCs) play a pivotal role in metastasis, the leading cause of cancer-associated death. Recent improvements of CTC isolation tools, coupled with a steady development of multiomics technologies at single-cell resolution, have enabled an extensive exploration of CTC biology, unlocking insights into their molecular profiles. A detailed molecular portrait requires CTC interrogation across various levels encompassing genomic, epigenetic, transcriptomic, proteomic and metabolic features...
April 5, 2024: Cancer Discovery
#38
JOURNAL ARTICLE
Arnault Tauziède-Espariat, Yvan Nicaise, Philipp Sievers, Felix Sahm, Andreas von Deimling, Delphine Guillemot, Gaëlle Pierron, Mathilde Duchesne, Myriam Edjlali, Volodia Dangouloff-Ros, Nathalie Boddaert, Alexandre Roux, Edouard Dezamis, Lauren Hasty, Benoît Lhermitte, Edouard Hirsch, Maria Paola Valenti Hirsch, François-Daniel Ardellier, Mélodie-Anne Karnoub, Marie Csanyi, Claude-Alain Maurage, Karima Mokhtari, Franck Bielle, Valérie Rigau, Thomas Roujeau, Marine Abad, Sébastien Klein, Michèle Bernier, Catherine Horodyckid, Clovis Adam, Petter Brandal, Pitt Niehusmann, Quentin Vannod-Michel, Corentin Provost, Nicolas Menjot de Champfleur, Lucia Nichelli, Alice Métais, Cassandra Mariet, Fabrice Chrétien, Thomas Blauwblomme, Kévin Beccaria, Johan Pallud, Stéphanie Puget, Emmanuelle Uro-Coste, Pascale Varlet
A novel methylation class, "neuroepithelial tumor, with PLAGL1 fusion" (NET-PLAGL1), has recently been described, based on epigenetic features, as a supratentorial pediatric brain tumor with recurrent histopathological features suggesting an ependymal differentiation. Because of the recent identification of this neoplastic entity, few histopathological, radiological and clinical data are available. Herein, we present a detailed series of nine cases of PLAGL1-fused supratentorial tumors, reclassified from a series of supratentorial ependymomas, non-ZFTA/non-YAP1 fusion-positive and subependymomas of the young...
April 5, 2024: Acta Neuropathologica Communications
#39
JOURNAL ARTICLE
Atsushi Hattori, Atsuhito Seki, Naoto Inaba, Kazuhiko Nakabayashi, Kazue Takeda, Kuniko Tatsusmi, Yasuhiro Naiki, Akie Nakamura, Keisuke Ishiwata, Kenji Matsumoto, Michiyo Nasu, Kohji Okamura, Toshimi Michigami, Yuko Katoh-Fukui, Akihiro Umezawa, Tsutomu Ogata, Masayo Kagami, Maki Fukami
All attempts to identify male-specific growth genes in humans have failed. This study aimed to clarify why men are taller than women. Microarray-based transcriptome analysis of the cartilage tissues of four adults and chondrocytes of 12 children showed that the median expression levels of SHOX, a growth gene in the pseudoautosomal region (PAR), were higher in male samples than in female samples. Male-dominant SHOX expression was confirmed by quantitative RT-PCR for 36 cartilage samples. Reduced representation bisulfite sequencing of four cartilage samples revealed sex-biased DNA methylation in the SHOX-flanking regions, and pyrosequencing of 22 cartilage samples confirmed male-dominant DNA methylation at the CpG sites in the SHOX upstream region and exon 6a...
April 5, 2024: Scientific Reports
#40
JOURNAL ARTICLE
Sara Rossi, Vanessa Tatangelo, Maria Dichiara, Stefania Butini, Sandra Gemma, Simone Brogi, Silvia Pasquini, Martina Cappello, Fabrizio Vincenzi, Katia Varani, Ludovica Lopresti, Margherita Malchiodi, Chiara Carrara, Alessandro Gozzetti, Monica Bocchia, Giuseppe Marotta, Laura Patrussi, Gabriele Carullo, Cosima T Baldari, Giuseppe Campiani
Chronic Lymphocytic Leukemia (CLL) patients have a defective expression of the proapoptotic protein p66Shc and of its transcriptional factor STAT4, which evoke molecular abnormalities, impairing apoptosis and worsening disease prognosis and severity. p66Shc expression is epigenetically controlled and transcriptionally modulated by STAT4; epigenetic modifiers are deregulated in CLL cells and specific histone deacetylases (HDACs) like HDAC1, are overexpressed. Reactivation of STAT4/p66Shc expression may represent an attractive and challenging strategy to reverse CLL apoptosis defects...
April 4, 2024: Biomedicine & Pharmacotherapy
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