Article
Oncology
Jennifer A. Karlow, Siddhartha Devarakonda, Xiaoyun Xing, Hyo Sik Jang, Ramaswamy Govindan, Mark Watson, Ting Wang
Summary: This study identified recurrent methylation patterns in brain metastases of non-small cell lung cancer (NSCLC), which may serve as prognostic biomarkers and contribute to disease progression. The altered DNA methylation was associated with the loss of EZH2 occupancy at developmental genes and changes in epigenetic regulation.
Article
Neurosciences
Wenping Ma, Zhaoshi Bao, Zenghui Qian, Kenan Zhang, Wenhua Fan, Jianbao Xu, Changyuan Ren, Ying Zhang, Tao Jiang
Summary: This study identified LRRFIP1 as a potential prognostic biomarker for glioma by analyzing the correlation between methylation genes and clinical prognosis in glioblastoma (GBM) patients. LRRFIP1 was found to be highly expressed in WHO IV, mesenchymal, and IDH wild-type subtypes. Additionally, GO and KEGG pathway analyses were performed to explore the functions and related mechanisms of LRRFIP1 in gliomas.
CNS NEUROSCIENCE & THERAPEUTICS
(2022)
Article
Medicine, Research & Experimental
Lin Xiang, La-Mei Chen, Yu-Jia Zhai, Wei-Juan Sun, Jie-Ru Yang, Yu-Chen Fan, Kai Wang
Summary: In patients with HBV-associated HCC, the methylation level of SFRP2 was significantly higher compared to CHB patients and healthy controls, while mRNA level of SFRP2 was significantly lower in HCC patients. Moreover, the combination of SFRP2 methylation level and AFP showed a significantly improved diagnostic value in discriminating HBV-associated HCC from CHB, suggesting the potential of SFRP2 methylation level as a non-invasive biomarker for HCC diagnosis.
Article
Biotechnology & Applied Microbiology
Hui Yang, Fei-Yang Na, Li Guo, Xuan Liang, Rong-Fang Zhang
Summary: This study investigated the contribution of DNA methylation to asthma and found that it can explain a portion of gene expression variability. Differential analysis identified HLA-DMB as a potential new biomarker for asthma, affected by abnormal DNA methylation. The study highlights the importance of DNA methylation in asthma development.
Review
Medicine, Research & Experimental
Dora Raos, Monika Ulamec, Ana Katusic Bojanac, Floriana Bulic-Jakus, Davor Jezek, Nino Sincic
Summary: RASSF1A, a tumor suppressor gene, is often inactivated in cancer through mutations and promoter hypermethylation. Current research focuses on its role as an epigenetic tumor biomarker.
BOSNIAN JOURNAL OF BASIC MEDICAL SCIENCES
(2021)
Article
Oncology
Xuan Li, Du Cai, Yaoyi Huang, Yumo Xie, Dingcheng Shen, Ze Yuan, Xiaoxia Liu, Meijin Huang, Yanxin Luo, Huichuan Yu, Xiaolin Wang
Summary: This study developed a DNA methylation biomarker to evaluate the prognosis of colorectal cancer (CRC) by identifying hypermethylated genes in cancer tissue from Illumina EPIC methylation arrays. The study found that RIMS2 was frequently hypermethylated and lowly expressed in CRC, and its methylation was associated with less frequent KRAS mutation and high differentiation. RIMS2 methylation showed independent predictive value for survival outcome and could predict prognosis better when combined with KRAS status.
Article
Immunology
Wei Chen, Yihuan Chen, Kai Zhang, Wanjing Yang, Xiang Li, Jun Zhao, Kangdong Liu, Ziming Dong, Jing Lu
Summary: CRC is a common aggressive tumor worldwide. This study identified AGT as a biomarker for diagnosis and prognosis in CRC, showing its role in promoting tumor progression. In vitro experiments revealed AGT's effects on CRC cell proliferation, migration, invasion, and angiogenesis, as well as its association with the drug ISL, which suppresses CRC cell progression.
INTERNATIONAL IMMUNOPHARMACOLOGY
(2021)
Article
Oncology
Peiru Liu, Jing Zhang, Duo Du, Dandan Zhang, Zelin Jin, Wenqing Qiu, Xiushi Zhou, Shulong Dong, Mengyu Zhou, Heyu Zhao, Wei Zhang, Jiakang Ma, Shaoyang Sun, Weiguo Fu, Yun Liu, Lixin Wang
Summary: This study revealed altered DNA methylation in TAD patients, with changes in gene expression related to vasculature and heart development, such as the Hox family genes. The cfDNA methylation pattern can serve as a highly disease-specific biomarker for TAD diagnosis, achieving both high sensitivity and specificity.
CLINICAL EPIGENETICS
(2021)
Article
Cell Biology
Xiaoqing Wu, Xuanren Shi, Xiaoyong Chen, Zhanhai Yin
Summary: AGEs can increase the expression of their receptor, RAGE, through downstream signaling pathways. The primary signaling pathways involved are NF-kappa B and STAT3. However, blocking these transcription factors does not fully inhibit the upregulation of RAGE, suggesting that AGEs may also affect RAGE expression through other pathways. In this study, we demonstrated that AGEs can induce epigenetic changes in RAGE expression.
FRONTIERS IN CELL AND DEVELOPMENTAL BIOLOGY
(2023)
Article
Genetics & Heredity
Shijin Yuan, Yuzhen Gao, Yan Xia, Zhuo Wang, Xian Wang
Summary: This study investigates the role of DNA methylation in tumor immunity and its impact on tumor microenvironment (TME) formation and immune activation. The researchers identified three DNA methylation modification patterns with distinct prognosis and biological behaviors, which correlated with three known phenotypes of immune-inflamed, immune-excluded, and immune-desert. They also demonstrated that a DNA methylation score (DMS) could be used as a predictive tool for immunotherapy. The findings provide valuable insights into TME immune infiltration characteristics and guide more effective and personalized immunotherapy strategies.
FRONTIERS IN GENETICS
(2022)
Article
Oncology
Arnaud Carrier, Cecile Desjobert, Valerie Lobjois, Lise Rigal, Florence Busato, Jorg Tost, Miquel Ensenyat-Mendez, Diego M. Marzese, Anne Pradines, Gilles Favre, Laurence Lamant, Luisa Lanfrancone, Chantal Etievant, Paola B. Arimondo, Joelle Riond
Summary: Protocadherin proteins play an important role in cell adhesion and signaling pathways. The study found that the PCDHB15 gene's specific exon is hypermethylated in melanoma, leading to its silencing. This silencing contributes to the aggressiveness of melanoma.
CLINICAL EPIGENETICS
(2022)
Article
Oncology
Nikola Zmarzly, Szymon Januszyk, Pawel Mieszczanski, Emilia Morawiec, Paulina Buda, Konrad Dziobek, Marcin Oplawski, Dariusz Boron
Summary: This study found that the expression of endothelins changes in endometrial cancer, and this may be mainly due to the silencing of EDN3 activity caused by DNA methylation.
JOURNAL OF CANCER RESEARCH AND CLINICAL ONCOLOGY
(2023)
Article
Biochemistry & Molecular Biology
Alexei J. Stuckel, Shuai Zengb, Zhen Lyub, Wei Zhang, Xu Zhang, Urszula Dougherty, Reba Mustafi, Tripti Khare, Qiong Zhang, Trupti Joshi, Marc Bissonnette, Sharad Khare
Summary: This study reports for the first time that SPRY4, which is frequently downregulated and considered as a tumor suppressor, is epigenetically upregulated in colorectal cancer (CRC). The promoter region of SPRY4 undergoes hypomethylation, while the gene body region shows decreased hydroxymethylation and increased methylation, which are correlated with increased expression in CRC patients.
Article
Oncology
Zhi Nie, Tong Pu, Zhaojie Han, Chenyang Wang, Chenglong Pan, Ping Li, Xiaoling Ma, Yanfei Yao, Youmei Zhao, Chunyan Wang, Xiulin Jiang, Jianyang Ding
Summary: This study investigated the expression level, prognostic values, diagnostic value, and immune infiltration level of Extra spindle pole bodies-like 1 (ESPL1) in lung adenocarcinoma (LUAD). The results showed that ESPL1 was upregulated in LUAD and its higher expression was associated with unfavorable prognosis and immune infiltration in LUAD. Additionally, ESPL1 expression was correlated with DNA copy number amplification and DNA hypo-methylation, and was involved in DNA replication and glycolysis signaling pathway. Knockdown of ESPL1 inhibited cell migration and invasion abilities of LUAD. These findings suggest that ESPL1 may serve as a novel prognostic biomarker for LUAD and be associated with immune cell infiltration.
FRONTIERS IN ONCOLOGY
(2022)
Article
Cell Biology
Chuan Zhang, Lu Wang, Chi Jin, Jiahui Zhou, Chaofan Peng, Yong Wang, Ziwei Xu, Dongsheng Zhang, Yuanjian Huang, Yue Zhang, Dongjian Ji, Wen Peng, Kangpeng Jin, Junwei Tang, Yifei Feng, Yueming Sun
Summary: Colorectal cancer is a common cancer worldwide, with liver metastasis being a key factor affecting prognosis. A study revealed that Lnc-LALC can regulate CRC cell metastasis ability by affecting DNA methylation status, highlighting its important role in CRLM.
CELL DEATH & DISEASE
(2021)
Editorial Material
Hematology
Maher K. Gandhi, Colm Keane
Letter
Pathology
Hemamal Samaratunga, Tony Gianduzzo, Joanna Perry-Keene, Lars Egevad, Brett Delahunt
Article
Biochemistry & Molecular Biology
Constantinos Constantinides, Laura K. M. Han, Clara Alloza, Linda Antonella Antonucci, Celso Arango, Rosa Ayesa-Arriola, Nerisa Banaj, Alessandro Bertolino, Stefan Borgwardt, Jason Bruggemann, Juan Bustillo, Oleg Bykhovski, Vince Calhoun, Vaughan Carr, Stanley Catts, Young-Chul Chung, Benedicto Crespo-Facorro, Covadonga M. Diaz-Caneja, Gary Donohoe, Stefan Du Plessis, Jesse Edmond, Stefan Ehrlich, Robin Emsley, Lisa T. Eyler, Paola Fuentes-Claramonte, Foivos Georgiadis, Melissa Green, Amalia Guerrero-Pedraza, Minji Ha, Tim Hahn, Frans A. Henskens, Laurena Holleran, Stephanie Homan, Philipp Homan, Neda Jahanshad, Joost Janssen, Ellen Ji, Stefan Kaiser, Vasily Kaleda, Minah Kim, Woo-Sung Kim, Matthias Kirschner, Peter Kochunov, Yoo Bin Kwak, Jun Soo Kwon, Irina Lebedeva, Jingyu Liu, Patricia Mitchie, Stijn Michielse, David Mothersill, Bryan Mowry, Victor Ortiz-Garcia de la Foz, Christos Pantelis, Giulio Pergola, Fabrizio Piras, Edith Pomarol-Clotet, Adrian Preda, Yann Quide, Paul E. Rasser, Kelly Rootes-Murdy, Raymond Salvador, Marina Sangiuliano, Salvador Sarro, Ulrich Schall, Andre Schmidt, Rodney J. Scott, Pierluigi Selvaggi, Kang Sim, Antonin Skoch, Gianfranco Spalletta, Filip Spaniel, Sophia Thomopoulos, David Tomecek, Alexander S. Tomyshev, Diana Tordesillas-Gutierrez, Therese van Amelsvoort, Javier Vazquez-Bourgon, Daniela Vecchio, Aristotle Voineskos, Cynthia S. Weickert, Thomas Weickert, Paul M. Thompson, Lianne Schmaal, Theo G. M. van Erp, Jessica Turner, James H. Cole, Danai Dima, Esther Walton
Summary: Schizophrenia patients show evidence of advanced brain ageing, which is not associated with clinical characteristics.
MOLECULAR PSYCHIATRY
(2023)
Review
Chemistry, Multidisciplinary
Kimberley Clack, Narshone Soda, Surasak Kasetsirikul, Rabbee G. G. Mahmudunnabi, Nam-Trung Nguyen, Muhammad J. A. Shiddiky
Summary: Liquid biopsy is a significant advancement in the early detection of cancer, as it offers painless sampling through easily accessible bodily fluids and eliminates the need for specialized equipment or trained staff. Nanotechnology and microfabrication have enabled the development of highly precise chip-based platforms, which can detect multiple cancer biomarkers simultaneously and overcome detection limitations. This review highlights the major advances in portable and semi-portable micro, nano, and multiplexed platforms for circulating cancer biomarker detection, discusses the merits and drawbacks of these platforms, and addresses the challenges and future directions in terms of device portability.
Article
Clinical Neurology
Mark K. Bakker, Jos P. Kanning, Gad Abraham, Amy E. Martinsen, Bendik S. Winsvold, John-Anker Zwart, Romain Bourcier, Tomonobu Sawada, Masaru Koido, Yoichiro Kamatani, Sandrine Morel, Philippe Amouyel, Stephanie Debette, Philippe Bijlenga, Takiy Berrandou, Santhi K. Ganesh, Nabila Bouatia-Naji, Gregory Jones, Matthew Bown, Gabriel J. E. HUNT All In Stroke, Jan H. CADISP Grp, Ynte M. Int Consortium Blood Pressure, Int Headache Genetics Consortium, ISGC, Intracranial Aneurysm Working Grp, Gabriel J. E. Rinkel, Jan Veldink, Ynte Ruigrok
Summary: Recently, common genetic risk factors for intracranial aneurysm (IA) and aneurysmal subarachnoid hemorrhage (ASAH) were found to have potential for genetic risk prediction. However, a genetic risk score incorporating these factors only showed limited predictive value for IA presence and ASAH incidence, suggesting that it may not be suitable for daily clinical use.
Article
Chemistry, Multidisciplinary
Junrong Li, Abu A. Sina, Fiach Antaw, David Fielding, Andreas Moller, Richard Lobb, Alain Wuethrich, Matt Trau
Summary: This study investigates the use of small extracellular vesicles (sEVs) molecular profiles in differentiating malignant and benign lung nodules via a liquid biopsy-based approach. The researchers develop a novel chip called DECODE that can analyze sEV biomarkers expression and generate digitally acquired sEV molecular profiles. The results show that DECODE can successfully separate malignant from benign lung nodules, suggesting its potential for non-invasive characterization of lung nodules found in lung cancer screening.
Article
Chemistry, Analytical
Mostak Ahmed, Alain Wuethrich, Nicolas Constantin, Karthik Balaji Shanmugasundaram, Paul Mainwaring, Arutha Kulasinghe, Connor O'Leary, Ken O'Byrne, Abu Ali Ibn Sina, Laura G. Carrascosa, Matt Trau
Summary: We developed a multiplexed phosphoprotein analyzer chip (MPAC) that enables rapid and sensitive detection of protein phosphorylation in lung cancer. Our study revealed that MPAC can monitor immunotherapy response by assessing the phosphorylation states of the proteins. The results suggest that phosphorylation levels are indicative of a positive response to therapy.
ANALYTICAL CHEMISTRY
(2023)
Article
Oncology
Jessica M. Logan, Ashley M. Hopkins, Carmela Martini, Alexandra Sorvina, Prerna Tewari, Sarita Prabhakaran, Chelsea Huzzell, Ian R. D. Johnson, Shane M. Hickey, Ben S. -Y. Ung, Joanna Lazniewska, Robert D. Brooks, Courtney R. Moore, Maria C. Caruso, Litsa Karageorgos, Cara M. Martin, Sharon O'Toole, Laura Bogue Edgerton, Mark P. Ward, Mark Bates, Stavros Selemidis, Adrian Esterman, Sheena Heffernan, Helen Keegan, Sarah Ni Mhaolcatha, Roisin O'Connor, Victoria Malone, Marguerite Carter, Katie Ryan, Andres Clarke, Nathan Brady, Sonja Klebe, Hemamali Samaratunga, Brett Delahunt, Michael J. Sorich, Kim Moretti, Lisa M. Butler, John J. O'Leary, Douglas A. Brooks
Summary: A novel biomarker panel (Appl1, Sortilin and Syndecan-1) was found to be a strong independent predictor for both clinical and biochemical recurrence outcomes, with higher prediction performance than traditional grading. The study also found that biomarker-assisted assessment had better predictive performance for evaluating the risk of biochemical recurrence and clinical recurrence in patients with prostate cancer.
Article
Biophysics
Md Sajedul Islam, Vinod Gopalan, Alfred K. Lam, Muhammad J. A. Shiddiky
Summary: Colorectal carcinoma (CRC) is a common cancer with high mortality rates, and various biomarkers and detection methods have been developed for its diagnosis and prognosis assessment. However, a gold standard method that is inexpensive, simple, and time-efficient and a critical review of the advantages and limitations of existing techniques are still lacking. This article provides an overview of the commonly used genetic and epigenetic biomarkers for CRC, discusses their detection methods, and presents the major challenges and advantages/limitations of current techniques.
BIOSENSORS & BIOELECTRONICS
(2023)
Review
Agriculture, Multidisciplinary
Tanzena Tanny, Mohamed Sallam, Narshone Soda, Nam-Trung Nguyen, Mobashwer Alam, Muhammad J. A. Shiddiky
Summary: The CRISPR/Cas system is an effective diagnostic tool for agricultural pathogens, providing high sensitivity, specificity, and rapid assay time. It is suitable for diagnosing plant pathogens and identifying genetically modified crops.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2023)
Letter
Pathology
Hemamali Samaratunga, Lars Egevad, Brett Delahunt
Review
Chemistry, Multidisciplinary
Cong Minh Nguyen, Mohamed Sallam, Md Sajedul Islam, Kimberley Clack, Narshone Soda, Nam-Trung Nguyen, Muhammad J. A. Shiddiky
Summary: Playing a critical role in fetal growth and development, the placenta serves as the interface between fetal and maternal circulation. Placental exosomes, small membrane-bound extracellular vesicles released by the placenta during pregnancy, contain biomolecules that can potentially be biomarkers for maternal diseases. Numerous studies have demonstrated the usefulness of placental exosomes in diagnosing and monitoring conditions such as pre-eclampsia and gestational diabetes, suggesting their potential as new biomarkers in liquid biopsy analysis. This review provides an overview of the biological function of placental exosomes, their potential as biomarkers for maternal diseases, and the current barriers and future directions in exosome isolation, characterization, and detection techniques. Additionally, microfluidic devices for exosome research are discussed.
Article
Nanoscience & Nanotechnology
Ramlah Khamis, Karthik B. Shanmugasundaram, Quan Zhou, Jennifer Lu, Zhen Zhang, Michelle M. Hill, Abu Ali Ibn Sina, Matt Trau, Alain Wuethrich
Summary: Endoscopy and tissue biopsy are the standard methods for diagnosing esophageal adenocarcinoma, but they are invasive and not suitable for population screening. In this study, a surface-enhanced Raman scattering lectin-immunoassay was developed to accurately measure serum levels of specific proteins. The results suggest that this method could be a promising liquid biopsy platform for screening esophageal adenocarcinoma.
ACS APPLIED NANO MATERIALS
(2023)
Article
Chemistry, Physical
Liwen Yuan, Yanpin Chen, Longfeng Ke, Quan Zhou, Jiayou Chen, Min Fan, Alain Wuethrich, Matt Trau, Jing Wang
Summary: Developing a minimally invasive technique for early-stage lung cancer detection is crucial. However, detecting rare tumor-associated extracellular vesicles (EVs) in blood remains challenging. In this study, we integrated gold core-silver shell nanoparticles and nanoscopic mixing in a microfluidic assay to accurately analyze EVs in plasma without pre-isolation. Our nanostrategy achieved high sensitivity and specificity in differentiating early-stage lung cancer from benign lung diseases, showing great potential for detecting the early occurrence of lung cancer.
NANOSCALE HORIZONS
(2023)