keyword
https://read.qxmd.com/read/38478332/cancer-stem-cells-current-challenges-and-future-perspectives
#21
REVIEW
Muhammad Vaseem Shaikh, Stefan Custers, Alisha Anand, Petar Miletic, Chitra Venugopal, Sheila K Singh
Despite major advances in health care including improved diagnostic tools, robust chemotherapeutic regimens, advent of precision, adjuvant and multimodal therapies, there is a major proportion of patients that still go on to experience tumor progression and recurrence. Cancer stem cells (CSCs) are shown to be responsible for tumor persistence and relapse. This subpopulation of cancer cells possess normal stem cell like traits of self-renewal, proliferation, and multilineage differentiation. Currently, they are isolated and enriched based on the cell surface markers that can be detected and sorted through fluorescence and magnetic-based cell sorting...
2024: Methods in Molecular Biology
https://read.qxmd.com/read/38477028/predicting-locus-specific-dna-methylation-levels-in-cancer-and-paracancer-tissues
#22
JOURNAL ARTICLE
Shuzheng Zhang, Baoshan Ma, Yu Liu, Yiwen Shen, Di Li, Shuxin Liu, Fengju Song
Aim: To predict base-resolution DNA methylation in cancerous and paracancerous tissues. Material & methods: We collected six cancer DNA methylation datasets from The Cancer Genome Atlas and five cancer datasets from Gene Expression Omnibus and established machine learning models using paired cancerous and paracancerous tissues. Tenfold cross-validation and independent validation were performed to demonstrate the effectiveness of the proposed method. Results: The developed cross-tissue prediction models can substantially increase the accuracy at more than 68% of CpG sites and contribute to enhancing the statistical power of differential methylation analyses...
March 13, 2024: Epigenomics
https://read.qxmd.com/read/38477016/construction-of-a-prognostic-model-based-on-genome-wide-methylation-analysis-of-mirnas-for-hepatocellular-carcinoma
#23
JOURNAL ARTICLE
Zhaoqi Shi, Xiaolong Liu, Duguang Li, Xiaoxiao Fan, Lifeng He, Daizhan Zhou, Hui Lin
Aim: Using the methylation level of miRNA genes to develop a prognostic model for patients with hepatocellular carcinoma (HCC). Materials & methods: least absolute shrinkage and selection operator and multivariate Cox regression analyses were performed to develop a prognostic model. One miRNA in the model was selected for verification. Results: A prognostic model was developed using eight miRNAs. The areas under the curve for predicting overall survival at 1, 3 and 5 years were 0.75, 0.81 and 0...
March 13, 2024: Epigenomics
https://read.qxmd.com/read/38473745/impact-of-histone-lysine-methyltransferase-suv4-20h2-on-cancer-onset-and-progression-with-therapeutic-potential
#24
REVIEW
Stela Papadaki, Christina Piperi
Histone lysine methyltransferase SUV4-20H2, a member of the suppressor of variegation 4-20 homolog (SUV4-20) family, has a critical impact on the regulation of chromatin structure and gene expression. This methyltransferase establishes the trimethylation of histone H4 lysine 20 (H4K20me3), a repressive histone mark that affects several cellular processes. Deregulated SUV4-20H2 activity has been associated with altered chromatin dynamics, leading to the misregulation of key genes involved in cell cycle control, apoptosis and DNA repair...
February 21, 2024: International Journal of Molecular Sciences
https://read.qxmd.com/read/38473261/targeted-dna-methylation-editing-using-an-all-in-one-system-establishes-paradoxical-activation-of-ebf3
#25
JOURNAL ARTICLE
Rakesh Banerjee, Priyadarshana Ajithkumar, Nicholas Keestra, Jim Smith, Gregory Gimenez, Euan J Rodger, Michael R Eccles, Jisha Antony, Robert J Weeks, Aniruddha Chatterjee
Cutaneous melanoma is rapidly on the rise globally, surpassing the growth rate of other cancers, with metastasis being the primary cause of death in melanoma patients. Consequently, understanding the mechanisms behind this metastatic process and exploring innovative treatments is of paramount importance. Recent research has shown promise in unravelling the role of epigenetic factors in melanoma progression to metastasis. While DNA hypermethylation at gene promoters typically suppresses gene expression, we have contributed to establishing the newly understood mechanism of paradoxical activation of genes via DNA methylation, where high methylation coincides with increased gene activity...
February 23, 2024: Cancers
https://read.qxmd.com/read/38471632/integrative-epigenome-transcriptome-analysis-unravels-cancer-specific-over-expressed-genes-potentially-regulating-immune-microenvironment-in-clear-cell-renal-cell-carcinoma
#26
JOURNAL ARTICLE
Nikhil Gadewal, Abhiram Natu, Siddhartha Sen, Sukanya Rauniyar, Virupaksha Bastikar, Sanjay Gupta
BACKGROUND: Clear cell Renal Cell Carcinoma (ccRCC) is the frequently diagnosed histological life-threatening tumor subtype in the urinary system. Integrating multi-omics data is emerging as a tool to provide a comprehensive view of biology and disease for better therapeutic interventions. METHOD: We have integrated freely available ccRCC data sets of genome-wide DNA methylome, transcriptome, and active histone modification marks, H3K27ac, H3K4me1, and H3K4me3 specific ChIP-seq data to screen genes with higher expression...
March 10, 2024: Biochimica et Biophysica Acta. General Subjects
https://read.qxmd.com/read/38471085/whole-genome-dna-methylation-profiling-of-intrahepatic-cholangiocarcinoma-reveals-prognostic-subtypes-with-distinct-biological-drivers
#27
JOURNAL ARTICLE
Haotian Liao, Xing Chen, Haichuan Wang, Youpei Lin, Lu Chen, Kefei Yuan, Mingheng Liao, Hanyu Jiang, Jiajie Peng, Zhenru Wu, Jiwei Huang, Jiaxin Li, Yong Zeng
Intrahepatic cholangiocarcinoma (iCCA) is the second most prevalent primary liver cancer. While the genetic characterization of iCCA has led to targeted therapies for treating tumors with FGFR2 alterations and IDH1/2 mutations, only a limited number of patients can benefit from these strategies. Epigenomic profiles have emerged as potential diagnostic and prognostic biomarkers for improving treatment of cancers. In this study, we conducted whole-genome bisulfite sequencing on 331 iCCAs integrated with genetic, transcriptomic, and proteomic analyses, demonstrating the existence of four DNA methylation subtypes of iCCAs (S1-S4) that exhibited unique post-operative clinical outcomes...
March 12, 2024: Cancer Research
https://read.qxmd.com/read/38466106/triterpenoid-ursolic-acid-regulates-the-environmental-carcinogen-benzo-a-pyrene-driven-epigenetic-and-metabolic-alterations-in-skh-1-hairless-mice-for-skin-cancer-interception
#28
JOURNAL ARTICLE
Md Shahid Sarwar, Christina N Ramirez, Hsiao-Chen Dina Kuo, Pochung Chou, Renyi Wu, Davit Sargsyan, Yuqing Yang, Ahmad Shannar, Rebecca Mary Peter, Ran Yin, Yujue Wang, Xiaoyang Su, Ah-Ng Kong
Polycyclic aromatic hydrocarbons (PAHs) are ubiquitous environmental carcinogens accountable to developing skin cancers. Recently, we reported that exposure to benzo[a]pyrene (B[a]P), a common PAH, causes epigenetic and metabolic alterations in the initiation, promotion, and progression of nonmelanoma skin cancer (NMSC). As a follow-up investigation, this study examines how dietary triterpenoid ursolic acid regulates B[a]P-driven epigenetic and metabolic pathways in SKH-1 hairless mice. Our results show UA intercepts against B[a]P-induced tumorigenesis at different stages of NMSC...
March 11, 2024: Carcinogenesis
https://read.qxmd.com/read/38460162/unveiling-alterations-of-epigenetic-modifications-and-chromatin-architecture-leading-to-lipid-metabolic-reprogramming-during-the-evolutionary-trastuzumab-adaptation-of-her2-positive-breast-cancer
#29
JOURNAL ARTICLE
Ningjun Duan, Yijia Hua, Xueqi Yan, Yaozhou He, Tianyu Zeng, Jue Gong, Ziyi Fu, Wei Li, Yongmei Yin
Secondary trastuzumab resistance represents an evolutionary adaptation of HER2-positive breast cancer during anti-HER2 treatment. Most current studies have tended to prioritize HER2 and its associated signaling pathways, often overlooking broader but seemingly less relevant cellular processes, along with their associated genetic and epigenetic mechanisms. Here, transcriptome data is not only characterized but also examined epigenomic and 3D genome architecture information in both trastuzumab-sensitive and secondary-resistant breast cancer cells...
March 9, 2024: Advanced Science (Weinheim, Baden-Wurttemberg, Germany)
https://read.qxmd.com/read/38450190/epigenetic-modifications-in-solid-tumor-metastasis-in-people-of-african-ancestry
#30
REVIEW
Elijah Kolawole Oladipo, Seun Elijah Olufemi, Daniel Adewole Adediran, Isaac Oluseun Adejumo, Esther Moderayo Jimah, Julius Kola Oloke, Chinedum C Udekwu, Olorunseun O Ogunwobi
This review focuses on the critical role of epigenetic modifications in solid tumor metastasis, particularly in people of African ancestry. Epigenetic alterations, such as DNA methylation, histone modifications, alterations in non-coding RNAs, and mRNA methylation, significantly influence gene expression, contributing to cancer development and progression. Despite the primary focus on populations of European, American, and Asian descent in most cancer research, this work emphasizes the importance of studying the unique genetic and epigenetic landscapes of African populations for a more inclusive approach in understanding and treating cancer...
2024: Frontiers in Oncology
https://read.qxmd.com/read/38448654/long-non-coding-rna-ccat1-acts-as-an-oncogene-to-promote-radiation-resistance-in-lung-adenocarcinoma-an-epigenomics-based-investigation
#31
JOURNAL ARTICLE
Jian Li, Shengnan Guo, Tianhao Li, Songliu Hu, Jianyu Xu, Xiangying Xu
Long non-coding RNAs (lncRNAs) appear to be the crucial modulators in various processes and critically influence the oncogenesis. As one of the LncRNAs, LncRNA CCAT1 has been reported to be closely associated with the progression multiple cancers, but its role in modulating the radioresistance of lung adenocarcinoma (LUAD) remains unclear. In our present study, we screened the potential radioresistance related LncRNAs in LUAD based on the data from The Cancer Genome Atlas (TCGA) database. Data suggested that CCAT1 was abundantly expressed in LUAD and CCAT1 was significantly associated with poor prognosis and radioresistance...
March 7, 2024: Functional & Integrative Genomics
https://read.qxmd.com/read/38447236/safeguarding-the-epigenome-through-the-cell-cycle-a-multitasking-game
#32
REVIEW
Valentin Flury, Anja Groth
Sustaining cell identity and function across cell division is germane to human development, healthspan, and cancer avoidance. This relies significantly on propagation of chromatin organization between cell generations, as chromatin presents a barrier to cell fate and cell state conversions. Inheritance of chromatin states across the many cell divisions required for development and tissue homeostasis represents a major challenge, especially because chromatin is disrupted to allow passage of the DNA replication fork to synthesize the two daughter strands...
April 2024: Current Opinion in Genetics & Development
https://read.qxmd.com/read/38445722/tutorial-on-survival-modeling-with-applications-to-omics-data
#33
JOURNAL ARTICLE
Zhi Zhao, John Zobolas, Manuela Zucknick, Tero Aittokallio
MOTIVATION: Identification of genomic, molecular and clinical markers prognostic of patient survival is important for developing personalized disease prevention, diagnostic and treatment approaches. Modern omics technologies have made it possible to investigate the prognostic impact of markers at multiple molecular levels, including genomics, epigenomics, transcriptomics, proteomics and metabolomics, and how these potential risk factors complement clinical characterization of patient outcomes for survival prognosis...
March 5, 2024: Bioinformatics
https://read.qxmd.com/read/38441107/epigenetic-dynamics-of-aging-and-cancer-development-current-concepts-from-studies-mapping-aging-and-cancer-epigenomes
#34
REVIEW
Shilpa Bisht, Yiqing Mao, Hariharan Easwaran
PURPOSE OF REVIEW: This review emphasizes the role of epigenetic processes as incidental changes occurring during aging, which, in turn, promote the development of cancer. RECENT FINDINGS: Aging is a complex biological process associated with the progressive deterioration of normal physiological functions, making age a significant risk factor for various disorders, including cancer. The increasing longevity of the population has made cancer a global burden, as the risk of developing most cancers increases with age due to the cumulative effect of exposure to environmental carcinogens and DNA replication errors...
March 1, 2024: Current Opinion in Oncology
https://read.qxmd.com/read/38438053/adipose-tissue-derived-stem-cells-in-vivo-and-in-vitro-models-for-metabolic-diseases
#35
REVIEW
Jaime Navarro-Perez, Stefania Carobbio
The primary role of adipose tissue stem cells (ADSCs) is to support the function and homeostasis of adipose tissue in physiological and pathophysiological conditions. However, when ADSCs become dysfunctional in diseases such as obesity and cancer, they become impaired, undergo signalling changes, and their epigenome is altered, which can have a dramatic effect on human health. In more recent years, the therapeutic potential of ADSCs in regenerative medicine, wound healing, and for treating conditions such as cancer and metabolic diseases has been extensively investigated with very promising results...
March 2, 2024: Biochemical Pharmacology
https://read.qxmd.com/read/38434768/leveraging-genomics-transcriptomics-and-epigenomics-to-understand-chemoimmunotherapy-resistance-in-chronic-lymphocytic-leukemia
#36
REVIEW
Shin Yeu Ong, Lili Wang
Patients with chronic lymphocytic leukemia (CLL) have differing clinical outcomes. Recent advances integrating multi-omic data have uncovered molecular subtypes in CLL with different prognostic implications and may allow better prediction of therapy response. While finite-duration chemoimmunotherapy (CIT) has enabled deep responses and prolonged duration of responses in the past, the advent of novel targeted therapy for the treatment of CLL has dramatically changed the therapeutic landscape. In this review, we discuss the latest genomic, transcriptomic, and epigenetic alterations regarded as major drivers of resistance to CIT in CLL...
2024: Cancer Drug Resistance
https://read.qxmd.com/read/38429759/epigenetic-remodeling-to-improve-the-efficacy-of-immunotherapy-in-human-glioblastoma-pre-clinical-evidence-for-development-of-new-immunotherapy-approaches
#37
JOURNAL ARTICLE
Maria Fortunata Lofiego, Francesca Piazzini, Francesca Pia Caruso, Francesco Marzani, Laura Solmonese, Emma Bello, Fabrizio Celesti, Maria Claudia Costa, Teresa Noviello, Roberta Mortarini, Andrea Anichini, Michele Ceccarelli, Sandra Coral, Anna Maria Di Giacomo, Michele Maio, Alessia Covre
BACKGROUND: Glioblastoma multiforme (GBM) is a highly aggressive primary brain tumor, that is refractory to standard treatment and to immunotherapy with immune-checkpoint inhibitors (ICI). Noteworthy, melanoma brain metastases (MM-BM), that share the same niche as GBM, frequently respond to current ICI therapies. Epigenetic modifications regulate GBM cellular proliferation, invasion, and prognosis and may negatively regulate the cross-talk between malignant cells and immune cells in the tumor milieu, likely contributing to limit the efficacy of ICI therapy of GBM...
March 1, 2024: Journal of Translational Medicine
https://read.qxmd.com/read/38429478/cancer-associated-fibroblast-derived-acetate-promotes-pancreatic-cancer-development-by-altering-polyamine-metabolism-via-the-acss2-sp1-sat1-axis
#38
JOURNAL ARTICLE
Divya Murthy, Kuldeep S Attri, Surendra K Shukla, Ravi Thakur, Nina V Chaika, Chunbo He, Dezhen Wang, Kanupriya Jha, Aneesha Dasgupta, Ryan J King, Scott E Mulder, Joshua Souchek, Teklab Gebregiworgis, Vikant Rai, Rohit Patel, Tuo Hu, Sandeep Rana, Sai Sundeep Kollala, Camila Pacheco, Paul M Grandgenett, Fang Yu, Vikas Kumar, Audrey J Lazenby, Adrian R Black, Susanna Ulhannan, Ajay Jain, Barish H Edil, David L Klinkebiel, Robert Powers, Amarnath Natarajan, Michael A Hollingsworth, Kamiya Mehla, Quan Ly, Sarika Chaudhary, Rosa F Hwang, Kathryn E Wellen, Pankaj K Singh
The ability of tumour cells to thrive in harsh microenvironments depends on the utilization of nutrients available in the milieu. Here we show that pancreatic cancer-associated fibroblasts (CAFs) regulate tumour cell metabolism through the secretion of acetate, which can be blocked by silencing ATP citrate lyase (ACLY) in CAFs. We further show that acetyl-CoA synthetase short-chain family member 2 (ACSS2) channels the exogenous acetate to regulate the dynamic cancer epigenome and transcriptome, thereby facilitating cancer cell survival in an acidic microenvironment...
March 1, 2024: Nature Cell Biology
https://read.qxmd.com/read/38427743/erratum-for-the-research-article-more-than-bad-luck-cancer-and-aging-are-linked-to-replication-driven-changes-to-the-epigenome-by-minteer-et-al
#39
JOURNAL ARTICLE
(no author information available yet)
No abstract text is available yet for this article.
March 2024: Science Advances
https://read.qxmd.com/read/38425402/multifaceted-role-of-micrornas-in-gastric-cancer-stem-cells-mechanisms-and-potential-biomarkers
#40
REVIEW
Qian-Hui Sun, Zi-Yu Kuang, Guang-Hui Zhu, Bao-Yi Ni, Jie Li
MicroRNAs (miRNAs) have received much attention in the past decade as potential key epigenomic regulators of tumors and cancer stem cells (CSCs). The abnormal expression of miRNAs is responsible for different phenotypes of gastric cancer stem cells (GCSCs). Some specific miRNAs could be used as promising biomarkers and therapeutic targets for the identification of GCSCs. This review summarizes the coding process and biological functions of miRNAs and demonstrates their role and efficacy in gastric cancer (GC) metastasis, drug resistance, and apoptosis, especially in the regulatory mechanism of GCSCs...
February 15, 2024: World Journal of Gastrointestinal Oncology
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