Article
Biochemistry & Molecular Biology
Darya Kaplun, Alexey Starshin, Fedor Sharko, Kristina Gainova, Galina Filonova, Nadezhda Zhigalova, Alexander Mazur, Egor Prokhortchouk, Svetlana Zhenilo
Summary: The gain and loss of DNA methylation in cells is a dynamic process that tends to reach equilibrium. Kaiso, in addition to being a methyl DNA binding protein, may attract methyltransferases to surrounding regions and modulate genome methylation in cells.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Biochemistry & Molecular Biology
Lingyuan Ma, Chenyu Li, Hanlin Yin, Jiashu Huang, Shenghao Yu, Jin Zhao, Yongxu Tang, Min Yu, Jie Lin, Lei Ding, Qinghua Cui
Summary: Breast cancer is the most common cancer worldwide, and its treatment methods include radiotherapy, chemotherapy, targeted therapy, and surgery. The molecular subtype of breast cancer determines the specific treatment measures, making the exploration of molecular mechanisms and therapeutic targets essential. Abnormal methylation of tumor suppressor genes by DNMTs is associated with poor prognosis in breast cancer. MiRNAs, as non-coding RNAs, play crucial roles in breast cancer and their aberrant methylation can lead to drug resistance. Therefore, regulating miRNA methylation could be a potential therapeutic target in breast cancer.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Andrea Palicelli, Stefania Croci, Alessandra Bisagni, Eleonora Zanetti, Dario De Biase, Beatrice Melli, Francesca Sanguedolce, Moira Ragazzi, Magda Zanelli, Alcides Chaux, Sofia Canete-Portillo, Maria Paola Bonasoni, Alessandra Soriano, Stefano Ascani, Maurizio Zizzo, Carolina Castro Ruiz, Antonio De Leo, Guido Giordano, Matteo Landriscina, Giuseppe Carrieri, Luigi Cormio, Daniel M. Berney, Jatin Gandhi, Davide Nicoli, Enrico Farnetti, Giacomo Santandrea, Martina Bonacini
Summary: Epigenetic alterations impact the expression of PD-L1 in prostate cancer, with DNA methylation and miRNAs being key factors. Histone modifiers and epigenetic drugs can reverse these alterations. miRNAs can regulate PD-L1 post-transcriptionally, offering potential clinical applications.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Review
Genetics & Heredity
Michela Saviana, Patricia Le, Lavender Micalo, Daniel Del Valle-Morales, Giulia Romano, Mario Acunzo, Howard Li, Patrick Nana-Sinkam
Summary: There is a crosstalk between DNA methylation and miRNA expression that plays a significant role in the pathogenesis of cancer. Understanding how miRNAs influence DNA methylation and vice versa is important for identifying therapeutic targets. Additionally, these epigenetic modifications may serve as potential biomarkers in cancer.
Article
Oncology
Ruth Pidsley, Dilys Lam, Wenjia Qu, Timothy J. Peters, Phuc-Loi Luu, Darren Korbie, Clare Stirzaker, Roger J. Daly, Phillip Stricker, James G. Kench, Lisa G. Horvath, Susan J. Clark
Summary: This study used methylome sequencing to investigate the DNA methylation patterns in prostate cancer patients, and identified methylation patterns associated with prostate cancer-specific mortality, as well as prognostic biomarkers. The combination of DNA methylation biomarkers and clinicopathological measures improved the prognostic models for prostate cancer mortality.
CLINICAL AND TRANSLATIONAL MEDICINE
(2022)
Review
Pharmacology & Pharmacy
Laboni Roy, Oishika Chatterjee, Debopriya Bose, Ananya Roy, Subhrangsu Chatterjee
Summary: The epigenetic landscape plays a crucial role in cellular homeostasis and its disruption can lead to cancer. Noncoding RNA networks, through regulation of processes like histone modification and DNA methylation, are key intracellular components involved in controlling cellular epigenetic characteristics. Understanding the effects of these RNA networks on epigenetic programming is important for the development of targeted cancer therapeutics.
DRUG DISCOVERY TODAY
(2023)
Article
Biochemistry & Molecular Biology
Tianxiao Huang, Yan Li, Wei Wang, Le Xu, Jingrui Li, Yijun Qi
Summary: This study reannotated lmiRNAs and their targets in rice, revealing that most lmiRNAs are derived from MITEs and suggesting co-evolution between lmiRNAs and their targets through MITE amplification. The study also found dynamic changes of lmiRNAs under stress conditions and enrichment of stress-responsive genes among lmiRNA targets, indicating the widespread involvement of lmiRNAs in plant stress responses. Furthermore, the study constructed the evolutionary histories of lmiRNAs and their targets, highlighting the importance of MITEs in the origin of lmiRNAs and suggesting a role for the evolution of lmiRNA-target regulatory modules in rice adaptation to environmental changes.
JOURNAL OF INTEGRATIVE PLANT BIOLOGY
(2022)
Article
Oncology
Mansheng Zhu, Qixiang Liang, Tao Chen, Qian Kong, Gengtai Ye, Shitong Yu, Xunjun Li, Qinglie He, Hao Liu, Yanfeng Hu, Jiang Yu, Guoxin Li
Summary: This study revealed the significant suppression of miRNA miR-129-2-3p in EBVaGC due to hypermethylation, and its role in promoting GC cell functions was demonstrated. The comprehensive analysis integrated multi-source data and provided insights into the relationships between methylated miRNA, differentially expressed genes (DEGs), and immune cell infiltration. Further experimental and clinical investigations are needed to validate these findings and explore the underlying mechanisms.
CLINICAL EPIGENETICS
(2021)
Review
Oncology
Weiwei Xie, Huizhen Sun, Xiaoduan Li, Feikai Lin, Ziliang Wang, Xipeng Wang
Summary: Ovarian cancer is associated with activation of oncogenes and inactivation of tumor suppressor genes, with epigenetic processes playing a key role in tumorigenesis. MicroRNA and long non-coding RNA are promising molecular markers for precision medicine in OC. Clinical application of epigenetic approaches is currently limited by hurdles such as heterogeneity of OC and insufficient sample sizes, but holds promise for future clinical investigation into diagnosis, treatment, and prognosis.
CANCER CELL INTERNATIONAL
(2021)
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
Medicine, Research & Experimental
Chun-Wu Pan, Simeng Wen, Lei Chen, Yulei Wei, Yuanjie Niu, Yu Zhao
Summary: In this study, it was found that antisense eRNA is regulated by androgen receptor activity in prostate cancer cells, negatively regulating antisense ncRNA in AR-related target genes' loci through DNA methylation. The chromatin interaction among enhancer, promoter, and gene-ending regions facilitated the expression of sense-eRNA and antisense-eRNA in cis, impacting cancer growth and patient outcomes. The suppression of antisense eRNA may serve as a potential novel target for improving prostate cancer therapy and diagnosis.
Review
Biochemistry & Molecular Biology
Jesus Porcuna, Jorge Minguez-Martinez, Mercedes Ricote
Summary: PPARs are ligand-modulated nuclear receptors involved in nutrient sensing, metabolism, and lipid-related processes. Dysregulation of PPAR-dependent transcriptional programs is linked to various diseases, and therapeutic exploitation of PPAR epigenetic modulation may provide new insights for treatment.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2021)
Article
Medicine, Research & Experimental
Erolcan Sayar, Radhika A. Patel, Ilsa M. Coleman, Martine P. Roudier, Ailin Zhang, Pallabi Mustafi, Jin-Yih Low, Brian Hanratty, Lisa S. Ang, Vipul Bhatia, Mohamed Adil, Hasim Bakbak, David A. Quigley, Michael T. Schweizer, Jessica E. Hawley, Lori Kollath, Lawrence D. True, Felix Y. Feng, Neil H. Bander, Eva Corey, John K. Lee, Colm Morrissey, Roman Gulati, Peter S. Nelson, Michael C. Haffner
Summary: Prostate-specific membrane antigen (PSMA) expression is heterogeneous in metastatic castration-resistant prostate cancer (mCRPC), with some cases showing no detectable PSMA and others showing heterogeneous expression across metastases. Loss of PSMA is associated with epigenetic changes, including CpG methylation and loss of H3K27 acetylation at the FOLH1 locus. Treatment with HDAC inhibitors can reverse this repression and restore PSMA expression. These findings provide insights into PSMA expression patterns and regulation in mCRPC, and suggest a potential therapeutic strategy using epigenetic therapies to augment PSMA levels.
Article
Pathology
Yuri Tolkach, Romina Zarbl, Simone Bauer, Manuel Ritter, Joerg Ellinger, Stephan Hauser, Laura Hueser, Sabine M. Klauck, Peter Altevogt, Holger Sultmann, Dimo Dietrich, Glen Kristiansen
Summary: CD24 is overexpressed in many human cancers, including prostate cancer, and its up-regulation can be influenced by DNA methylation of the CD24 promoter. Higher levels of CD24 expression are associated with poorer outcomes in prostate cancer patients, including shorter biochemical recurrence-free survival. Overexpression of ERG and PTEN deficiency are also correlated with increased CD24 expression levels in prostate cancer.
AMERICAN JOURNAL OF PATHOLOGY
(2021)
Article
Endocrinology & Metabolism
Mousa Vatanmakanian, Joshua J. Steffan, Sweaty Koul, Augusto C. Ochoa, Lakshmi S. Chaturvedi, Hari K. Koul
Summary: Prostate cancer progression is characterized by decreased SPDEF expression due to hypermethylation, which can be partially reversed through inhibition of DNMTs. This study highlights the important role of epigenetic regulation in prostate cancer development and suggests DNMTs as a potential therapeutic target for limiting tumor progression and therapy resistance.
FRONTIERS IN ENDOCRINOLOGY
(2023)
Article
Surgery
Solange Bayard, Laura Susick, Ishmael Kyei, Yalei Chen, Melissa B. Davis, Kofi Gyan, Lisa A. Newman
AMERICAN JOURNAL OF SURGERY
(2020)
Article
Oncology
Jung S. Byun, Sandeep K. Singhal, Samson Park, Dae Ik Yi, Tingfen Yan, Ambar Caban, Alana Jones, Partha Mukhopadhyay, Sara M. Gil, Stephen M. Hewitt, Lisa Newman, Melissa B. Davis, Brittany D. Jenkins, Jorge L. Sepulveda, Adriana De Siervi, Anna Maria Napoles, Nasreen A. Vohra, Kevin Gardner
CLINICAL CANCER RESEARCH
(2020)
Letter
Surgery
Yalei Chen, Laura Susick, Melissa Davis, Jessica Bensenhaver, S. David Nathanson, Jessica Burns, Lisa A. Newman
Article
Biotechnology & Applied Microbiology
Kiumars Badr, William Whelan, Q. Peter He, Jin Wang
Summary: Recent research has shown that synthetic methanotroph-photoautotroph cocultures have great potential for converting biogas into valuable products. An experimental-computational protocol has been proposed to quantitatively characterize these cocultures and determine key parameters accurately and efficiently.
BIOTECHNOLOGY AND BIOENGINEERING
(2021)
Review
Oncology
Rachel Martini, Lisa Newman, Melissa Davis
Summary: Breast cancer mortality is 40% higher among African American women compared to their White counterparts in the US, primarily driven by tumor characteristics rather than socio-economic factors. Despite similar incidence rates, African American women still have higher mortality rates across all breast cancer subtypes.
CLINICAL & EXPERIMENTAL METASTASIS
(2022)
Article
Engineering, Environmental
Kiumars Badr, Q. Peter He, Jin Wang
Summary: By developing an experimental-computational protocol, a kinetic model for M-P cocultures was established to accurately predict growth dynamics under various conditions. The study confirmed the presence of additional emergent metabolic exchanges within the coculture and quantified their impact on the growth of both species in the model coculture, supporting further research in metabolic engineering.
CHEMICAL ENGINEERING JOURNAL
(2022)
Article
Oncology
Daisy B. Haigh, Corinne L. Woodcock, Jennifer Lothion-Roy, Anna E. Harris, Veronika M. Metzler, Jenny L. Persson, Brian D. Robinson, Francesca Khani, Mansour Alsaleem, Atara Ntekim, Srinivasan Madhusudan, Melissa B. Davis, Kristian B. Laursen, Lorraine J. Gudas, Catrin S. Rutland, Michael S. Toss, Nathan Archer, Zsuzsanna Bodi, Emad A. Rakha, Rupert G. Fray, Jennie N. Jeyapalan, Nigel P. Mongan
Summary: This study investigated whether therapies targeting the epitranscriptome can suppress androgen signalling in prostate cancer. The results showed that METTL3 is aberrantly expressed in prostate cancer patients and that knockdown or inhibition of METTL3 can significantly alter the basal and androgen-regulated transcriptome in prostate cancer, suggesting that targeting m6A could be a novel approach to modulate androgen signalling in prostate cancer.
Article
Oncology
Md Shakir Uddin Ahmed, Brittany D. Lord, Benjamin Adu Addai, Sandeep K. Singhal, Kevin Gardner, Ahmad Bin Salam, Anghesom Ghebremedhin, Jason White, Iqbal Mahmud, Rachel Martini, Deepa Bedi, Huixian Lin, Jacqueline D. Jones, Balasubramanyanam Karanam, Windy Dean-Colomb, William Grizzle, Honghe Wang, Melissa Davis, Clayton C. Yates
Summary: African American women with breast cancer have higher inflammation and a stronger immune response than European American women. The biological role of Kaiso in immune signaling was demonstrated in breast cancer exosomes. Kaiso depletion reduced tumor formation and increased infiltration of M1 macrophages.
Article
Biotechnology & Applied Microbiology
Jangwon Lee, Ankur Kumar, Jesus Flores-Cerrillo, Jin Wang, Q. Peter He
Summary: Pressure swing adsorption (PSA) is widely used for gas product separation, but monitoring the process can be challenging due to its complexity and lack of steady state. To address these challenges, a feature-based statistical process monitoring (SPM) framework called feature space monitoring (FSM) is proposed, which demonstrates superior performance in early fault detection compared to traditional SPM methods.
FRONTIERS IN CHEMICAL ENGINEERING
(2022)
Proceedings Paper
Automation & Control Systems
Kiumars Badr, Q. Peter He, Jin Wang
Summary: The study investigates the potential emergent metabolic interactions within a Methanotroph-Photoautotroph (M-P) coculture through experiments and semi-structured kinetic modeling. The researchers successfully confirmed the existence of additional interspecies metabolic interactions and developed a genome-scale model for the M-P coculture. The findings provide insights into the metabolic dynamics and growth enhancement of the coculture.
Proceedings Paper
Automation & Control Systems
Jangwon Lee, Zhuoxiong Sun, Tai B. Tan, Jorge Mendez, Jesus Flores-Cerrillo, Jin Wang, Q. Peter He
Summary: Rotating machines, such as pumps and compressors, are critical components in refinery and chemical plants. Estimating the remaining useful life (RUL) of bearings is crucial for reducing production losses and avoiding machine damage. Data-driven approaches have been widely used due to the complexity and stochastic nature of bearing failure mechanisms.
Article
Multidisciplinary Sciences
Kiumars Badr, Q. Peter He, Jin Wang
Summary: This paper presents the matlab implementation details of a novel semi-structured kinetic model for methanotroph-photoautotroph cocultures. The model is validated using a wide range of experimental conditions and accurately predicts the growth of the coculture and changes in gas composition over time. It explicitly models the exchange of in situ produced O-2 and CO2 within the coculture and considers the self-shading effect on the growth of photoautotroph.
Proceedings Paper
Automation & Control Systems
Jangwon Lee, Ankur Kumar, Jesus Flores-Cerrillo, Jin Wang, Q. Peter He
Proceedings Paper
Automation & Control Systems
Jangwon Lee, Jin Wang, Jesus Flores-Cerrillo, Q. Peter He
Proceedings Paper
Automation & Control Systems
Kerul Suthar, Jin Wang, Zhihua Jiang, Q. Peter He
2020 AMERICAN CONTROL CONFERENCE (ACC)
(2020)