Review
Oncology
Asad Mohammad, Sudhakar Jha
Summary: Epigenetic modifications, such as DNA methylation and histone modification, play a crucial role in cancer progression and metastasis. Inhibitors targeting deregulated enzymes can reverse these modifications and show promising results in cancer therapeutics.
Article
Genetics & Heredity
Bradley P. Balaton, Carolyn J. Brown
Summary: X-chromosome inactivation is a common epigenetic phenomenon in XX eutherian mammals, where some genes can escape inactivation and remain expressed. Research shows that heterochromatic marks are less enriched and euchromatic marks are more depleted on the active X chromosome in genes that have undergone inactivation.
EPIGENETICS & CHROMATIN
(2021)
Article
Psychiatry
Oluwagbenga Dada, Christopher Adanty, Nasia Dai, Richie Jeremian, Sauliha Alli, Philip Gerretsen, Ariel Graff, John Strauss, Vincenzo De Luca
Summary: The study found evidence of epigenetic age acceleration associated with psychosis severity in individuals with schizophrenia, using two different algorithms for DNAm age analysis.
PSYCHIATRY RESEARCH
(2021)
Article
Biochemistry & Molecular Biology
Laetitia P. Meyrueix, Raad Gharaibeh, Jing Xue, Cory Brouwer, Corbin Jones, Linda Adair, Shane A. Norris, Folami Ideraabdullah
Summary: This study defined the DNA methylome of GDM placentas and identified changes in methylation at genes important for placental development. The findings revealed extensive changes in the placental epigenome of GDM pregnancies, particularly in genes related to placental development pathways. These molecular changes may serve as potential biomarkers for placental, maternal, and fetal health.
Article
Immunology
Krisann K. Oursler, Vincent C. Marconi, Zeyuan Wang, Ke Xu, Monty Montano, Kaku So-Armah, Amy C. Justice, Yan Sun
Summary: The associations between epigenetic age acceleration markers and physiologic frailty and mortality in people with HIV provide insight into accelerated aging and support the development of interventions for preventing and treating age-related diseases in this population.
CLINICAL INFECTIOUS DISEASES
(2023)
Article
Biotechnology & Applied Microbiology
Aditya S. Deshpande, Netha Ulahannan, Matthew Pendleton, Xiaoguang Dai, Lynn Ly, Julie M. Behr, Stefan Schwenk, Will Liao, Michael A. Augello, Carly Tyer, Priyesh Rughani, Sarah Kudman, Huasong Tian, Hannah G. Otis, Emily Adney, David Wilkes, Juan Miguel Mosquera, Christopher E. Barbieri, Ari Melnick, David Stoddart, Daniel J. Turner, Sissel Juul, Eoghan Harrington, Marcin Imielinski
Summary: The study reveals the significance of high-order three-dimensional chromatin interactions in gene regulation. By developing Pore-C and Chromunity, researchers are able to analyze high-order chromatin contacts at the genome scale and find their enrichment in enhancers and promoters in active chromatin as well as highly transcribed and lineage-defining genes.
NATURE BIOTECHNOLOGY
(2022)
Article
Geriatrics & Gerontology
Fedor Galkin, Polina Mamoshina, Kirill Kochetov, Denis Sidorenko, Alex Zhavoronkov
Summary: DNA methylation aging clocks have become an invaluable tool in biogerontology research, with deep learning showing promise as an accurate method for predicting age. The newly presented DeepMAge clock demonstrates biological relevance by assigning higher predicted age to individuals with certain health-related conditions.
Article
Psychology, Clinical
Anthony S. Zannas, Sarah D. Linnstaedt, Xinming An, Jennifer S. Stevens, Nathaniel G. Harnett, Alyssa R. Roeckner, Katelyn I. Oliver, David R. Rubinow, Elisabeth B. Binder, Karestan C. Koenen, Kerry J. Ressler, Samuel A. McLean
Summary: Psychological trauma exposure and PTSD are associated with advanced epigenetic age. This study found that epigenetic age measured at the time of trauma may predict the subsequent development of PTSD. The neural substrates underlying posttraumatic outcomes associated with epigenetic aging are unclear.
PSYCHOLOGICAL MEDICINE
(2023)
Article
Cell Biology
Guyanan Li, Chenming Wang, Xin Guan, Yansen Bai, Yue Feng, Wei Wei, Hua Meng, Ming Fu, Meian He, Xiaomin Zhang, Yanjun Lu, Yong Lin, Huan Guo
Summary: This study aimed to investigate the role of sex chromosomes in the aging process and discovered age-related DNA methylation changes on the Y chromosome. The findings suggest that certain methylation levels of specific genes are associated with male aging and all-cause mortality risk.
Article
Cell & Tissue Engineering
Atsushi Fukuda, Dane Z. Hazelbaker, Nami Motosugi, Jin Hao, Francesco Limone, Amanda Beccard, Patrizia Mazzucato, Angelica Messana, Chisa Okada, Irune Guerra San Juan, Menglu Qian, Akihiro Umezawa, Hidenori Akutsu, Lindy E. Barrett, Kevin Eggan
Summary: The study found that de novo DNA methyltransferases DNMT3A/3B are crucial for repressing XIST in female hPSCs, and the maintenance of XIST silencing is independent of de novo DNA methylation.
Article
Genetics & Heredity
Man Li, Litao Bao, Ping Zhu, Shuxia Wang
Summary: This study investigated the impact of metformin on the epigenetic age in subjects with type 2 diabetes mellitus (DM). The results showed an association between metformin intake and slower epigenetic aging.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
Qi Gao, Fang Chen, Lijun Zhang, Ai Wei, Yongxiang Wang, Zhiwei Wu, Wangsen Cao
Summary: In this study, it was found that DNA methylation alterations in renal aging play significant roles, with suppression of NRF2 and KLOTHO leading to elevated DNMT expression and gene promoter hypermethylation. Treatment with DNMT inhibitor or natural polyphenol oleuropein reversed the epigenetic suppression of antiaging factors and mitigated structural and functional changes in aging kidneys.
Article
Biology
Devika Singh, Dan Sun, Andrew G. King, David E. Alquezar-Planas, Rebecca N. Johnson, David Alvarez-Ponce, Soojin Yi
Summary: This study investigates the DNA methylation patterns in a male and female koala across five tissues, revealing the distinct features of DNA methylation in marsupials. It shows that females have a significant global reduction in X chromosome DNA methylation compared to males and identifies sex-specific methylation patterns upstream of the lncRNA associated with marsupial XCI. The findings suggest evolutionary divergent pathways leading to functionally conserved patterns of XCI in mammals.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2021)
Article
Genetics & Heredity
Janine M. LaSalle
Summary: The article discusses the etiology of autism spectrum disorders and the role of DNA methylation in this process. By studying X chromosome inactivation mechanisms, it reveals the challenges and unanswered questions in studying human development, such as biased sex ratios and male bias.
FRONTIERS IN GENETICS
(2022)
Article
Biochemical Research Methods
Pegah Mavaie, Lawrence Holder, Daniel Beck, Michael K. Skinner
Summary: This study introduced a hybrid DL-ML approach to predict environmentally responsive transgenerational differential DNA methylated regions using deep neural network for feature extraction and a non-DL classifier. The experimental results showed that this approach outperforms traditional deep learning and machine learning methods.
BMC BIOINFORMATICS
(2021)
Article
Genetics & Heredity
Francesco Ravaioli, Michele Zampieri, Luca Morandi, Chiara Pirazzini, Camilla Pellegrini, Sara De Fanti, Noemie Gensous, Gian Luca Pirazzoli, Luisa Sambati, Alessandro Ghezzo, Fabio Ciccarone, Anna Reale, Daniela Monti, Stefano Salvioli, Paola Caiafa, Miriam Capri, Alexander Buerkle, Maria Moreno-Villanueva, Paolo Garagnani, Claudio Franceschi, Maria Giulia Bacalini
Summary: This study investigated the DNA methylation and RNA expression levels of rDNA genes in adults with Down syndrome (DS). The results showed that the promoter region of rDNA tends to be hypermethylated in DS, leading to lower intra-individual diversity and lower RNA expression levels. These findings suggest a rearrangement of the epigenetic profile of rDNA in DS to compensate for the excess rDNA copies.
FRONTIERS IN GENETICS
(2022)
Article
Cell Biology
D. F. Durso, G. Silveira-Nunes, M. M. Coelho, G. C. Camatta, L. H. Ventura, L. S. Nascimento, F. Caixeta, E. H. M. Cunha, A. Castelo-Branco, D. M. Fonseca, T. U. Maioli, A. Teixeira-Carvalho, C. Sala, M. J. Bacalini, P. Garagnani, C. Nardini, C. Franceschi, A. M. C. Faria
Summary: Living in endemic areas for chronic infectious diseases results in remodeling of inflammaging and acceleration of epigenetic aging in individuals regardless of their infectious status.
MECHANISMS OF AGEING AND DEVELOPMENT
(2022)
Article
Endocrinology & Metabolism
Peter Lauffer, Nitash Zwaveling-Soonawala, Shaobo Li, Maria G. Bacalini, Oxana Y. Naumova, Joseph Wiemels, Anita Boelen, Peter Henneman, Adam J. de Smith, A. S. Paul van Trotsenburg
Summary: In Down syndrome, there is a high occurrence of congenital hypothyroidism and subclinical hypothyroidism. This study found that promoter region hypermethylation of thyroid-related genes may cause transcriptional downregulation, leading to the occurrence of congenital hypothyroidism and subclinical hypothyroidism in Down syndrome.
Article
Cell Biology
Angelica Giuliani, Maria Giulia Bacalini, Deborah Ramini, Emanuela Mensa, Chiara Giordani, Luciano Xumerle, Paolo Garagnani, Fabiola Olivieri, Antonio Domenico Procopio, Maria Rita Rippo, Jacopo Sabbatinelli
Summary: Bone marrow mesenchymal stromal cells (BMSCs) have the ability to self-renew and differentiate into adipocytes and osteoblasts, but the role of DNA methylation in their function and replicative senescence is still unclear. A genome-wide DNA methylation analysis revealed genome-wide hypomethylation and overlapping differentially methylated positions (DMPs) in replicative senescent BMSCs and HUVECs. Pathway analysis identified common pathways associated with senescence, insulin resistance, molecule adhesion, and Wnt/beta-catenin signaling. This study provides valuable insights into the mechanisms of replicative senescence and BMSC differentiation.
Article
Biochemistry & Molecular Biology
Angelica Giuliani, Jacopo Sabbatinelli, Stefano Amatori, Laura Graciotti, Andrea Silvestrini, Giulia Matacchione, Deborah Ramini, Emanuela Mensa, Francesco Prattichizzo, Lucia Babini, Domenico Mattiucci, Elena Marinelli Busilacchi, Maria Giulia Bacalini, Emma Espinosa, Fabrizia Lattanzio, Antonio Domenico Procopio, Fabiola Olivieri, Antonella Poloni, Mirco Fanelli, Maria Rita Rippo
Summary: This study found that the expression of MeCP2 protein is downregulated during adipogenic differentiation of hBMSCs. This downregulation is not dependent on MeCP2 DNA methylation or mRNA levels, but on miRNA regulation. miR-422a and miR-483-5p are upregulated during adipogenic differentiation of hBMSCs. Modulation of miR-422a and miR-483-5p levels can affect MeCP2 expression and adipogenic differentiation.
CELLULAR AND MOLECULAR LIFE SCIENCES
(2023)
Article
Biochemistry & Molecular Biology
Maria Maddalena Tumedei, Filippo Piccinini, Irene Azzali, Francesca Pirini, Sara Bravaccini, Serena De Matteis, Claudio Agostinelli, Gastone Castellani, Michele Zanoni, Michela Cortesi, Barbara Vergani, Biagio Eugenio Leone, Simona Righi, Anna Gazzola, Beatrice Casadei, Davide Gentilini, Luciano Calzari, Francesco Limarzi, Elena Sabattini, Andrea Pession, Marcella Tazzari, Clara Bertuzzi
Summary: The majority of patients with Follicular Lymphoma (FL) experience subsequent phases of remission and relapse, making the disease virtually incurable. Clinical-based prognostic scores have been proposed to predict the outcome of FL patients at diagnosis, but they continue to fail for a subset of patients. Gene expression profiling has highlighted the pivotal role of the tumor microenvironment (TME) in the FL prognosis, but there is still a need to standardize the assessment of immune-infiltrating cells for prognostic classification.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Review
Biochemistry & Molecular Biology
Giovanni Vitale, Silvia Carra, Ylenia Alessi, Federica Campolo, Carla Pandozzi, Isabella Zanata, Annamaria Colao, Antongiulio Faggiano
Summary: Carcinoid syndrome is a debilitating paraneoplastic disease occurring in 10-40% of patients with neuroendocrine tumors. Its main symptoms include flushing, diarrhea, hypotension, tachycardia, bronchoconstriction, venous telangiectasia, dyspnea, and fibrotic complications. Although there are drugs available, lack of therapeutic response and resistance remain challenges. Preclinical models serve as crucial tools for studying tumor progression and developing new therapies. This paper provides an overview of in vitro and in vivo models in NETs with carcinoid syndrome and discusses future developments and therapeutic approaches.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Cell Biology
Katarzyna Malgorzata Kwiatkowska, Eleni Mavrogonatou, Adamantia Papadopoulou, Claudia Sala, Luciano Calzari, Davide Gentilini, Maria Giulia Bacalini, Daniele Dall'Olio, Gastone Castellani, Francesco Ravaioli, Claudio Franceschi, Paolo Garagnani, Chiara Pirazzini, Dimitris Kletsas
Summary: The aim of this study was to characterize DNA methylation patterns in replicative and induced senescence in different human cell types. Three epigenetic signatures were identified: cell type- and treatment-specific signature, cell type-specific senescence-related signature, and cell type-transversal replicative senescence-related signature. Cluster analysis revealed distinct DNA methylation patterns in replicative senescent cells, and enrichment in pathways related to the nervous system was shown. Despite no statistically significant evidence of age acceleration, a trend of increased biological age in replicative senescent cultures of all three cell types was observed. This work highlights the heterogeneity of senescent cells and their impact on tissue homeostasis.
Article
Neurosciences
Luca Baldelli, Chiara Pirazzini, Luisa Sambati, Francesco Ravaioli, Davide Gentilini, Giovanna Calandra-Buonaura, Pietro Guaraldi, Claudio Franceschi, Pietro Cortelli, Paolo Garagnani, Maria Giulia Bacalini, Federica Provini
Summary: Isolated REM Sleep Behavior Disorder (iRBD) serves as a strong early indicator for alpha-synucleinopathies. However, little research has been done on the relationship between aging and prodromal phases of neurodegenerative diseases. This study used epigenetic clocks based on DNA methylation to measure biological aging in iRBD patients, as well as videopolysomnography-negative and population-based controls. The findings suggest that accelerated aging is a characteristic of prodromal neurodegeneration in iRBD patients.
NPJ PARKINSONS DISEASE
(2023)
Article
Cell Biology
Clement Crochemore, Claudia Chica, Paolo Garagnani, Giovanna Lattanzi, Steve Horvath, Alain Sarasin, Claudio Franceschi, Maria Giulia Bacalini, Miria Ricchetti
Summary: Cockayne syndrome (CS) and UV-sensitive syndrome (UVSS) are rare genetic disorders caused by mutation of the DNA repair and multifunctional CSA or CSB protein. CS displays a progeroid and neurodegenerative phenotype, and differential analysis of DNA methylation (DNAm) revealed a CS-specific epigenomic signature enriched in developmental transcription factors, ion/neurotransmitter membrane transporters and synaptic neuro-developmental genes. CS also exhibited epigenetic hallmarks of accelerated ageing, including hypomethylation of Alu sequences and increased biological age compared to healthy and UVSS cells.
Article
Oncology
Alessandra Dicitore, Germano Gaudenzi, Silvia Carra, Maria Celeste Cantone, Monica Oldani, Davide Saronni, Maria Orietta Borghi, Jacopo Grotteschi, Luca Persani, Giovanni Vitale
Summary: This study investigated the potential antitumor effects of axitinib on lung carcinoid cells using both in vitro and in vivo models. Axitinib demonstrated significant antitumor activity by reducing cell viability, inducing cell cycle arrest, and promoting cell death. It also had a notable impact on tumor-induced angiogenesis and invasiveness.
Article
Health Care Sciences & Services
Keenan A. Ramsey, Carel G. M. Meskers, Marijke C. Trappenburg, Maria Giulia Bacalini, Massimo Delledonne, Paolo Garagnani, Carolyn Greig, Victor Kallen, Nico van Meeteren, Natal van Riel, Nadine Correia Santos, Sarianna Sipila, Janice L. Thompson, Anna C. Whittaker, Andrea B. Maier
Summary: The PANINI Toolkit aims to provide a standardized assessment tool for evaluating multiple domains of health in older adults, with a focus on nutrition and physical activity. It was developed through consensus of experts within the PANINI consortium and has been implemented successfully in various countries and populations.
Article
Endocrinology & Metabolism
Biagio Cangiano, Emanuele Giusti, Caterina Premoli, Davide Soranna, Giovanni Vitale, Silvia Grottoli, Valeria Cambria, Giovanna Mantovani, Roberta Mungari, Pietro Maffei, Francesca Dassie, Antonella Giampietro, Sabrina Chiloiro, Maria Laura Tanda, Silvia Ippolito, Salvatore Cannavo, Marta Ragonese, Antonella Zambon, Luca Persani, Letizia Maria Fatti, Massimo Scacchi
Summary: This study found a high prevalence of depression in patients with acromegaly, which is associated with female gender and arthropathy. Both depression and arthropathy independently and strongly contribute to the impaired quality of life in patients.
Article
Endocrinology & Metabolism
Alessandra Dicitore, Maria Giulia Bacalini, Davide Saronni, Germano Gaudenzi, Maria Celeste Cantone, Giulia Gelmini, Elisa Stellaria Grassi, Davide Gentilini, Maria Orietta Borghi, Anna Maria Di Blasio, Luca Persani, Paolo Garagnani, Claudio Franceschi, Giovanni Vitale
Summary: The study found that the demethylating agent and methyl donor showed significant antitumor activity in DU-145 and PC-3 cells, through perturbation of cell cycle progression, induction of apoptosis, and inhibition of cell migration. These drugs reversed neuroendocrine transdifferentiation and modified DNA methylation pattern, particularly affecting pathways involved in cell proliferation, apoptosis, and cell migration.
NEUROENDOCRINOLOGY
(2022)
