Article
Gastroenterology & Hepatology
Long Long Cao, Heng Lu, Mohammed Soutto, Nadeem Bhat, Zheng Chen, Dunfa Peng, Ahmed Gomaa, Jia Bin Wang, Jian Wei Xie, Ping Li, Chao Hui Zheng, Sachiyo Nomura, Jashodeep Datta, Nipun Merchant, Zhi Bin Chen, Alejandro Villarino, Alexander Zaika, Chang Ming Huang, Wael El-Rifai
Summary: This study developed a classification method based on immune cell infiltration to classify GC and found that immune desert-type and excluded-type tumors are resistant to ICB therapy compared to immune-inflamed tumors. The study also identified the enrichment of epithelial-mesenchymal transition (EMT) signaling in immune desert-type GC, and showed that mesenchymal-like tumors in syngeneic mice exhibited T cell-exclusion and resistance to CTLA4 blockade.
Review
Oncology
Jacek Baj, James Curtis Dring, Marcin Czeczelewski, Pawel Kozyra, Alicja Forma, Jolanta Flieger, Beata Kowalska, Grzegorz Buszewicz, Grzegorz Teresinski
Summary: Micro- and nanoplastic particles pose a significant threat to human health, potentially leading to the development of various types of cancers. Extensive research has been conducted to investigate the effects of exposure to these substances, revealing a clear correlation between micro- and nanoplastic exposure and the onset of several cancers.
Article
Gastroenterology & Hepatology
Carolina F. Ruivo, Nuno Bastos, Barbara Adem, Ines Batista, Cecilia Duraes, Carlos A. Melo, Stephanie A. Castaldo, Francisco Campos-Laborie, Pedro Moutinho-Ribeiro, Barbara Morao, Ana Costa-Pinto, Soraia Silva, Hugo Osorio, Sergio Ciordia, Jose Luis Costa, David Goodrich, Bruno Cavadas, Luisa Pereira, Tony Kouzarides, Guilherme Macedo, Rui Maio, Fatima Carneiro, Marilia Cravo, Raghu Kalluri, Jose Carlos Machado, Sonia A. Melo
Summary: This study reveals that pancreatic ductal adenocarcinoma (PDAC) tumors establish a communication network mediated by cancer stem cells (CSC) and the protein agrin, which promotes tumor growth and therapy resistance. CSC release extracellular vesicles (EVs) that activate specific proteins, leading to increased tumor cell proliferation and transcriptional regulator activation. Targeting this communication network may provide a potential strategy for targeted therapy and has significant implications for cancer stem cells.
Article
Biochemical Research Methods
Desmond O. Agwunobi, Mengxue Li, Ningmei Wang, Guomin Chang, Xiaojing Zhang, Xiaomin Xue, Zhijun Yu, Hui Wang, Jingze Liu
Summary: This study investigated the molecular mechanism of lemongrass essential oil on the Haemaphysalis longicornis tick using proteomic analysis. Pathway analysis revealed the activation of metabolic pathways mediated by oxidoreductases and transferases. Furthermore, evidence of cytotoxic mode of action was found, involving reactive oxygen species, mitochondrial calcium overload, mitochondrial uncoupling, depolarization, and ATP depletion. The RNAi of a major detoxification enzyme also caused morphological alterations, which requires further investigation.
Article
Gastroenterology & Hepatology
Heng Lu, Long Long Cao, Farah Ballout, Abbes Belkhiri, Dunfa Peng, Lei Chen, Zheng Chen, Mohammed Soutto, Timothy C. Wang, Jianwen Que, Silvia Giordano, Mary Kay Washington, Steven Chen, Oliver Gene Mcdonald, Alexander Zaika, Wael El-Rifai
Summary: This study revealed the role of acidic bile salts (ABS) in promoting epithelial-mesenchymal transition (EMT) in oesophageal adenocarcinoma (EAC) through APE1 redox-dependent E-cadherin cleavage. The findings suggest that APE1-redox inhibitors could be a therapeutic option for EAC treatment.
Article
Environmental Sciences
Si-si Chen, Tian-qi Wang, Wan-chen Song, Zhi-jie Tang, Zhao-ming Cao, Hong-juan Chen, Yi Lian, Xin Hu, Wei-juan Zheng, Hong-zhen Lian
Summary: This study proposes a novel PM sampling and cell exposure strategy based on agar membrane. The agar membrane is proven to be a reliable substitute material for PM sampling, and the extracted PM from the agar membrane shows higher cytotoxicity and more differentially expressed proteins compared to the traditional extraction method.
Review
Oncology
Abdul Arif Khan
Summary: Colorectal cancer originates from polyps, and research has identified key targets and pathways associated with the transformation of polyps into cancer. Functional overrepresentation analysis has provided insights into the overall mechanism.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2021)
Article
Multidisciplinary Sciences
Ryan O. Schencka, Eunjung Kim, Rafael R. Bravo, Jeffrey West, Simon Leedham, Darryl Shibata, Alexander R. A. Anderson
Summary: Recent studies have found that normal human tissues accumulate somatic mutations, especially in human skin, which contains multiple subclones of different sizes. Driver mutations are frequent and have larger subclone sizes, suggesting selection. Using a simple agent-based skin-cell model, researchers have shown that these complex somatic mutations can be explained by the model's prime directive of homeostasis. The model replicates the observed log-linear distributions of somatic mutations, where most mutations are found in increasingly smaller subclones that are typically lost over time. The model also suggests that the accumulation of more frequent and larger driver subclones can occur if these mutations confer higher persistence in normal skin or during tissue damage.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2022)
Article
Oncology
Jun-ichi Akagi, Young-Man Cho, Takeshi Toyoda, Yasuko Mizuta, Kumiko Ogawa
Summary: The phosphorylated form of histone H2AX (gamma-H2AX) is commonly used as a biomarker for DNA damage. This study found that gamma-H2AX foci formation was not effectively induced by hepatocarcinogens that did not stimulate hepatocyte proliferation. Instead, increased expressions of EpCAM and APN were observed in hepatocytes, suggesting their potential as alternative biomarkers for detecting chemical hepatocarcinogenicity in combination with gamma-H2AX.
Review
Biochemistry & Molecular Biology
Caio Bezerra Machado, Leidivan Sousa da Cunha, Jersey Heitor da Silva Maues, Flavia Melo Cunha de Pinho Pessoa, Marcelo Braga de Oliveira, Rodrigo Monteiro Ribeiro, Germison Silva Lopes, Manoel Odorico de Moraes Filho, Maria Elisabete Amaral de Moraes, Andre Salim Khayat, Caroline Aquino Moreira-Nunes
Summary: This study analyzed the deregulated miRNA expression in HTLV-1 infected cells and patients' samples and identified 12 miRNAs and 90 genes with significant biological interactions that may play a role in the onset of ATL. These miRNAs and genes are associated with key signaling pathways.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Review
Multidisciplinary Sciences
Farizatul Akmawati Yahya, Nur Fariesha Md Hashim, Daud Ahmad Israf Ali, Tham Chau Ling, Manraj Singh Cheema
Summary: Toxicology aims to understand and predict the adverse effects of chemicals and xenobiotics on biological systems. Systems toxicology, utilizing systems biology, can extrapolate and interrelate vast biological system data to better comprehend toxicology-related questions. Shifting from empirical, animal-based testing to a mechanistic understanding is essential for future advancements in toxicology.
JOURNAL OF KING SAUD UNIVERSITY SCIENCE
(2021)
Article
Cell Biology
Sara Abdelfatah, Janine Nass, Caroline Knorz, Sabine M. Klauck, Jan-Heiner Kuepper, Thomas Efferth
Summary: Pyrrolizidine alkaloids are highly toxic compounds found as contaminants in food and medicines. This study used a transcriptomic approach to investigate the effects of PAs on liver cells, revealing disruptions in important signaling pathways and potential carcinogenic effects. The findings suggest that PAs have mutagenic properties and can disturb cell cycle regulation, leading to cell damage and potentially carcinogenesis.
CELL BIOLOGY AND TOXICOLOGY
(2022)
Article
Chemistry, Multidisciplinary
Giorgia La Barbera, Katrine Dalmo Nommesen, Catalina Cuparencu, Jan Stanstrup, Lars Ove Dragsted
Summary: The field of DNA adductomics aims to screen known and unknown DNA adducts in biological samples. However, the lack of databases and bioinformatics tools in this field limits its applicability. This paper presents a four-step approach to compile and curate a database for the annotation of DNA adducts in biological samples, providing a powerful tool for (HR)MS-based DNA adduct annotation.
FRONTIERS IN CHEMISTRY
(2022)
Article
Biotechnology & Applied Microbiology
Francesco Marchetti, Renato Cardoso, Connie L. Chen, George R. Douglas, Joanne Elloway, Patricia A. Escobar, Tod Harper Jr, Robert H. Heflich, Darren Kidd, Anthony M. Lynch, Barbara L. Parsons, Jesse J. Salk, Raja S. Settivari, Stephanie L. Smith-Roe, Kristine L. Witt, Carole L. Yauk, Robert Young, Shaofei Zhang, Sheroy Minocherhomji
Summary: Error-corrected Next Generation Sequencing (ecNGS) is a valuable and accurate method for detecting and characterizing mutations in any DNA-isolable cell type, tissue, or organism. It has potential applications in genotoxicity assessment, mutagenesis studies in 3D organotypic cultures, and detecting off-target effects of gene editing tools. It can also be used to measure early biomarkers and mutational load in human biomonitoring studies.
MUTATION RESEARCH-REVIEWS IN MUTATION RESEARCH
(2023)
Article
Chemistry, Analytical
Adam Witmer, Bir Bhanu
Summary: This paper presents a method of dataset augmentation using generative adversarial networks (GAN) to improve the classification accuracy of deep convolutional neural networks (CNN) trained on induced pluripotent stem cell microscopy images. By addressing the lack of data through generated images and employing a hierarchical classification scheme and domain knowledge, improvements in accuracy are achieved.