Article
Biochemistry & Molecular Biology
Aleksandra Gorska, Maria Urbanowicz, Lukasz Grochowalski, Michal Seweryn, Marta Sobalska-Kwapis, Tomasz Wojdacz, Magdalena Lange, Marta Gruchala-Niedoszytko, Justyna Jarczak, Dominik Strapagiel, Magdalena Gorska-Ponikowska, Iwona Pelikant-Malecka, Leszek Kalinowski, Boguslaw Nedoszytko, Danuta Gutowska-Owsiak, Marek Niedoszytko
Summary: This study aimed to identify the differential methylation profiles and gene expression patterns associated with mastocytosis, a heterogenous disease of the mast cells. Genome-wide DNA methylation analysis was performed on peripheral blood samples from mastocytosis patients and healthy controls. The results showed significant differences in methylation levels of selected regions, including 31 genes located within the regulatory regions. Additionally, three oncogenes-FOXQ1, TWIST1, and ERG-were found to be differentially methylated in mastocytosis patients for the first time. These findings provide insights into the methylation landscape of mastocytosis and potential therapeutic targets.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2023)
Article
Medicine, Research & Experimental
Xianghai Liao, Peter J. Kennel, Bohao Liu, Trevor R. Nash, Richard Z. Zhuang, Amandine F. Godier-Furnemont, Chenyi Xue, Rong Lu, Paolo C. Colombo, Nir Uriel, Muredach P. Reilly, Steven O. Marx, Gordana Vunjak-Novakovic, Veli K. Topkara
Summary: Heart failure (HF) is characterized by global alterations in myocardial DNA methylation, and this study investigates the epigenetic regulation of the noncoding genome and reversibility of DNA methylation with LVAD therapy. Mapping of myocardial DNA methylation in HF patients at LVAD implantation and explantation, as well as nonfailing donors, identifies differentially methylated positions (DMPs) in ischemic and nonischemic cardiomyopathy. LVAD support results in normalization of a small percentage of HF-associated DMPs, and analysis reveals genes that are hypomethylated and upregulated or hypermethylated and downregulated in HF. Additionally, a cardiac-specific super-enhancer lncRNA is found to be hypermethylated and downregulated in human HF and is an upstream regulator of gene expression related to sarcomere and calcium channels. These findings suggest that HF-associated changes in DNA methylation are minimally reversible with mechanical unloading, and epigenetic reprogramming may be necessary for sustained clinical recovery from heart failure.
Article
Obstetrics & Gynecology
Min Yang, Xin Tao, Katherine Scott, Yiping Zhan, Richard T. Scott, Emre Seli
Summary: The study revealed that embryos with different developmental potentials exhibit different DNA methylation profiles at the blastocyst stage, indicating a potential negative correlation between genome-wide methylation level and embryo quality.
HUMAN REPRODUCTION
(2021)
Article
Biology
Junying Wang, Wen Zhang, Xiaoqin Liu, Minjee Kim, Ke Zhang, Robert Y. L. Tsai
Summary: This study identified differentially methylated genomic regions (DMRs) in mouse livers that are co-regulated by aging and regeneration using whole-genome bisulfite sequencing (WGBS). The DMRs showed opposite methylation direction changes between 2 and 8 months and 8 and 16 months. Inverse-regulated DMRs by aging and regeneration were found in the promoter/gene regions of 12 genes. These findings provide insights into the epigenomic changes underlying the biology of aging on liver regeneration.
Review
Biochemistry & Molecular Biology
Xiancan Wang, Xianghai Kong, Xin Feng, Ding-Sheng Jiang
Summary: Ferroptosis is a type of programmed cell death characterized by increased levels of ferrous ions and lipid peroxidation. It has been found to play a role in various organ injuries and degenerative diseases, while insufficient ferroptosis has been linked to tumorigenesis. The regulatory mechanisms of ferroptosis involve iron metabolism, redox systems, and epigenetic mechanisms. This review provides a critical analysis of the molecular mechanisms and regulatory networks of ferroptosis, with a focus on the role of DNA, RNA, and protein methylation. The unanswered questions and debated findings in this field are also discussed.
INTERNATIONAL JOURNAL OF BIOLOGICAL SCIENCES
(2023)
Article
Nutrition & Dietetics
Olga Sularz, Aneta Koronowicz, Cayla Boycott, Sylwester Smolen, Barbara Stefanska
Summary: The study evaluated the effect of iodine-biofortified lettuce on anti-tumor properties in human gastrointestinal cancer cell lines. The results showed that extracts from iodine-biofortified lettuce reduced the viability and proliferation of gastric and colon cancer cells. The extracts also affected cell cycle and protein expression, mediating the anti-tumor effects.
Article
Oncology
Xiaonan Liu, Pei Wang, Xufei Teng, Zhang Zhang, Shuhui Song
Summary: This study characterized the expression profiles of RNA m6A regulators in 13 cancer types using TCGA data, revealing potential regulatory mechanisms of miRNA and DNA methylation in governing m6A regulators' expression. Informative regulatory pairs with potential prognostic values were identified, providing new insights into the molecular mechanisms of m6A modification in human cancers.
FRONTIERS IN ONCOLOGY
(2021)
Article
Biochemistry & Molecular Biology
Glen E. Duncan, Ally Avery, Millissia Ben Maamar, Eric E. Nilsson, Daniel Beck, Michael K. Skinner
Summary: This study aimed to identify potential systemic DNA methylation alterations associated with obesity using an epigenome-wide association approach. The results demonstrate the feasibility of identifying systemic epigenetic biomarkers for obesity, which may have implications for preventative medicine and clinical management of the disease.
Article
Immunology
Xiaoqing Xu, Yuxi Zhang, Zhaobing Pan, Xiaojing Zhang, Xiaonan Liu, Lili Tang, Xiaoguang Zhang, Fusheng Zhou, Hui Cheng
Summary: In this study, Munro's microabscess was found to be associated with 647 differentially methylated sites. Further analysis revealed that DNA methylation might affect the physical properties associated with skin cells and recruit neutrophils in the epidermis through pathways such as cell-substrate junction and focal adhesion.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biochemistry & Molecular Biology
Aaron John Stevens, Lucy de Jong, Martin Alexander Kennedy
Summary: DNA modifications, such as methylation, may act as a dynamic switch to promote or alleviate the formation of G-quadruplex structures. The interaction between epigenetic DNA modifications, G4 formation, and the 3D architecture of the genome is a complex and developing area of research. Such interactions could represent novel mechanisms for important biological functions.
INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES
(2022)
Article
Multidisciplinary Sciences
Hongxu Ding, Ioannis Anastopoulos, Andrew D. Bailey, Joshua Stuart, Benedict Paten
Summary: This study introduces a deep learning framework that can predict the characteristic ionic currents of nucleotides to enable novel detection of nucleotide modifications, particularly methylated cytosine and guanine, without the need for controls.
NATURE COMMUNICATIONS
(2021)
Article
Medicine, General & Internal
Andres Esteban-Cantos, Javier Rodriguez-Centeno, Juan C. Silla, Pilar Barruz, Fatima Sanchez-Cabo, Gabriel Saiz-Medrano, Julian Nevado, Beatriz Mena-Garay, Maria Jimenez-Gonzalez, Rosa de Miguel, Jose I. Bernardino, Roco Montejano, Julen Cadinanos, Cristina Marcelo, Lucia Gutierrez-Garcia, Patricia Martinez-Martin, Cedrick Wallet, Francois Raffi, Berta Rodes, Jose R. Arribas
Summary: This study investigates the effects of antiretroviral therapy (ART) on HIV-induced epigenetic modifications. It found that ART initiation modified DNA methylation levels at 845 CpG positions, with 49.3% of the changes being restored to the uninfected state. Untreated HIV infection was associated with DNA methylation changes in biological processes regulating the immune system and antiviral responses. Changes in DNA methylation levels after ART initiation were weakly correlated with changes in CD4+ cell counts and the CD4/CD8 ratio.
Article
Gastroenterology & Hepatology
Runhua Lin, Yanli Qian, Jinhai Zhang, Di Xia, Dongming Guo, Liangli Hong, Bojuan Qing, Muming Xu, Yiteng Huang, Wenting Lin, Guangcan Chen, Shuhui Liu
Summary: This study identifies DNA methylation aberrations in gastric cardia cancer (GCC) and demonstrates that ADHFE1 gene DNA methylation contributes to the risk of GCC. These findings provide novel mechanistic insights into gastric cardia cancer carcinogenesis.
JOURNAL OF GASTROENTEROLOGY AND HEPATOLOGY
(2023)
Article
Immunology
Qi Chen, Hao Li, Yusi Liu, Min Zhao
Summary: This study comprehensively analyzed the epigenetic regulation in rheumatoid arthritis (RA) using differential analysis and cross-analysis. The results identified differentially methylated sites, differentially expressed genes, and differentially expressed miRNAs associated with RA. A comprehensive epigenetic regulatory network was constructed, and core regulatory genes were identified. This study provides a new direction for future research on the epigenetic mechanisms of RA.
FRONTIERS IN IMMUNOLOGY
(2022)
Article
Biology
Paula Esteller-Cucala, Marc Palmada-Flores, Lukas F. K. Kuderna, Claudia Fontsere, Aitor Serres-Armero, Marc Dabad, Maria Torralvo, Armida Faella, Luis Ferrandez-Peral, Laia Llovera, Oscar Fornas, Eva Julia, Erika Ramirez, Irene Gonzalez, Jochen Hecht, Esther Lizano, David Juan, Tomas Marques-Bonet
Summary: This study generates genome assemblies for seven major haplogroups of the human Y chromosome at a unique resolution that overcomes the structurally complex regions within. These data enable the detection and profiling of epigenetic modifications among the considered haplogroups.
COMMUNICATIONS BIOLOGY
(2023)
Editorial Material
Immunology
Eva Kaufmann, Marija Landekic, Jeffrey Downey, Julia Chronopoulos, Sara Teimouri Nezhad, Kim Tran, Donald C. Vinh, Luis B. Barreiro, Maziar Divangahi
Article
Biology
Noah D. Simons, Vasiliki Michopoulos, Mark Wilson, Luis B. Barreiro, Jenny Tung
Summary: Variation in social status can impact gene regulation, glucocorticoid physiology, and mitochondrial DNA phenotypes in animals. Behavioral interactions associated with dominance rank play a significant role in these effects, often serving as better predictors of molecular and physiological outcomes than dominance rank itself.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES
(2022)
Article
Biochemistry & Molecular Biology
Amanda J. Lea, Julie Peng, Julien F. Ayroles
Summary: In addition to genotype and environment, most complex traits are also influenced by poorly understood interactions between these two factors. This study mapped the genetic basis of gene expression levels across different cellular environments and revealed that these interactions have an evolutionary component.
Article
Medicine, General & Internal
Ian J. Wallace, Amanda J. Lea, Yvonne A. L. Lim, Steven K. W. Chow, Izandis bin Mohd Sayed, Romano Ngui, Mohd Tajudin Haji Shaffee, Kee-Seong Ng, Colin Nicholas, Vivek V. Venkataraman, Thomas S. Kraft
Summary: This study aims to investigate the prevalence and environmental causes of non-communicable diseases (NCDs) among the indigenous peoples of Peninsular Malaysia, known as Orang Asli. The project will collect biospecimens and conduct screening for NCDs, combined with ethnographic work to assess lifestyle and sociocultural variables. The study will examine the relationship between environmental changes and NCD susceptibility, as well as the molecular and physiological mechanisms that mediate environmental effects on health. It will also identify factors, both intrinsic and extrinsic, that predispose certain individuals to NCDs in the face of environmental change.
Article
Genetics & Heredity
Luisa F. F. Pallares, Amanda J. J. Lea, Clair Han, Elena V. V. Filippova, Peter Andolfatto, Julien F. F. Ayroles
Summary: Evolutionary theory suggests that lifespan-reducing alleles should be eliminated, but studies have shown that they persist. This study found that alleles regulating lifespan have context-dependent effects and a third of lifespan-associated genetic variation is influenced by the environment. Lifespan-reducing alleles are often recent, have stronger effects on a high-sugar diet, and show signs of selection in wild populations, supporting the evolutionary mismatch hypothesis. These findings provide insights into the complex genetic architecture of lifespan and the evolutionary processes that shape it.
Article
Multidisciplinary Sciences
Amanda J. Lea, Angela Garcia, Jesusa Arevalo, Julien F. Ayroles, Kenneth Buetow, Steve W. Cole, Daniel Eid Rodriguez, Maguin Gutierrez, Heather M. Highland, Paul L. Hooper, Anne Justice, Thomas Kraft, Kari E. North, Jonathan Stieglitz, Hillard Kaplan, Benjamin C. Trumble, Michael D. Gurven
Summary: Research has found that putatively selected alleles are associated with phenotypes in underrepresented populations, such as Amerindians, and may uncover new loci underlying evolutionarily and biomedically relevant traits. By combining anthropological and biomedical data, researchers have identified gene regions related to immune and metabolic function.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2023)
Article
Ecology
Emily M. McLean, Jacob A. Moorad, Jenny Tung, Elizabeth A. Archie, Susan C. Alberts
Summary: This study investigates the role of genetic variance in shaping affiliative behaviors in the Amboseli wild baboon population. The results show that grooming behavior in female baboons is heritable and influenced by environmental factors such as dominance rank and the availability of kin as grooming partners. There is also a small but measurable genetic effect of partner identity on grooming behavior.
Article
Zoology
Sam K. Patterson, Rachel M. Petersen, Lauren J. N. Brent, Noah Snyder-Mackler, Amanda J. Lea, James P. Higham
Summary: Adverse experiences in early life have been found to be associated with aging-related disease risk and mortality in various species. However, due to confounding factors and difficulties in direct measurement, it is challenging to determine the impact of early life adversity on aging and health in humans. Studying non-human animals, which experience similar forms of adversity and age similarly to humans, can help overcome these challenges. Additionally, studying the links between early life adversity and aging in natural populations of non-human animals provides insights into the social and ecological pressures that influenced the evolution of early life sensitivities.
INTEGRATIVE AND COMPARATIVE BIOLOGY
(2023)
Article
Multidisciplinary Sciences
Elizabeth C. Lange, Shuxi Zeng, Fernando A. Campos, Fan Li, Jenny Tung, Elizabeth A. Archie, Susan C. Alberts
Summary: Adverse conditions in early life can negatively affect adult health and survival in humans and other animals. This study examines the mediating role of adult social behavior in the relationship between early adversity and adult survival. The results suggest that early adversity and adult sociality have independent effects on survival, and strong social bonds and high social status can mitigate the negative effects of early adversity. These findings highlight the importance of affiliative social behavior in natural selection and provide potential targets for intervention to improve human health and well-being.
Editorial Material
Ecology
Christina A. A. Del Carpio, Ashlyn T. T. Ford, Eva S. Horna Lowell, Marissa E. E. Ochoa, Hayden P. P. Speck
Summary: Seminar series play a crucial role in academic culture. We propose strategies to enhance diversity of seminar speakers, aiming to provide more opportunities for members in the field of ecology and evolutionary biology research.
NATURE ECOLOGY & EVOLUTION
(2023)
Article
Behavioral Sciences
Jenny Tung, Elizabeth C. Lange, Susan C. Alberts, Elizabeth A. Archie
Summary: Field studies of wild baboons in Kenya's Amboseli ecosystem over the past five decades have revealed profound associations between early life adversity, adult social conditions, and key aging outcomes, particularly survival. The study found that early adversity, social isolation, and glucocorticoids are independently linked to adult lifespans, suggesting potential for mitigating the negative consequences of early life adversity. Additionally, the study explores the evolutionary rationale for early life effects on mortality and highlights important themes and open questions for future research.
NEUROSCIENCE AND BIOBEHAVIORAL REVIEWS
(2023)
Article
Biochemistry & Molecular Biology
Amanda J. Lea, Andrew G. Clark, Andrew W. Dahl, Orrin Devinsky, Angela R. Garcia, Christopher D. Golden, Joseph Kamau, Thomas S. Kraft, Yvonne A. L. Lim, Dino J. Martins, Donald Mogoi, Paeivi Pajukanta, George H. Perry, Herman Pontzer, Benjamin C. Trumble, Samuel S. Urlacher, Vivek V. Venkataraman, Ian J. Wallace, Michael Gurven, Daniel E. Lieberman, Julien F. Ayroles
Summary: Noncommunicable diseases (NCDs) such as obesity, cardiovascular disease, and type 2 diabetes are increasing worldwide. The evolutionary mismatch hypothesis suggests that human evolution occurred in environments different from the one we live in today, leading to traits that were advantageous in the past becoming mismatched and disease-causing. By combining genomic tools with partnerships with subsistence-level groups undergoing rapid lifestyle changes, we can identify genetic loci associated with disease risk and gain insights into NCDs across diverse ancestries and cultures.
Article
Genetics & Heredity
Scott S. Wolf, Diogo Melo, Kristina M. S. Garske, Luisa F. Pallares, Amanda J. S. Lea, Julien F. Ayroles
Summary: This study investigates gene expression variance and finds that it is consistent across different tissues and datasets. Low-variance genes are associated with fundamental cell processes and have lower genetic polymorphisms, while high-variance genes are enriched for immune response and environmentally responsive genes. These results suggest that gene expression variance is a functionally constrained gene trait with important implications for understanding complex traits and disease.
Article
Multidisciplinary Sciences
Benjamin C. C. Trumble, Mia Charifson, Tom Kraft, Angela R. R. Garcia, Daniel K. K. Cummings, Paul Hooper, Amanda J. J. Lea, Daniel Eid Rodriguez, Stephanie V. V. Koebele, Kenneth Buetow, Bret Beheim, Riana Minocher, Maguin Gutierrez, Gregory S. S. Thomas, Margaret Gatz, Jonathan Stieglitz, Caleb E. E. Finch, Hillard Kaplan, Michael Gurven
Summary: A study found that Tsimane women with the APOE-e4 gene have higher fertility, start reproducing at an earlier age, and have shorter interbirth intervals. This finding supports the need for researching how genes that are harmful in urban environments have been maintained throughout human evolutionary history in ancestrally relevant environments.
Article
Anthropology
Arielle S. Fogel, Peter O. Oduor, Albert W. Nyongesa, Charles N. Kimwele, Susan C. Alberts, Elizabeth A. Archie, Jenny Tung
Summary: The study quantified the risk of fetal loss in wild hybrid baboons and examined the factors that contribute to it. Contrary to the hypothesis, genetic ancestry did not predict fetal loss in hybrid females. Instead, ecological factors and female age were found to be the key determinants of fetal loss.
AMERICAN JOURNAL OF BIOLOGICAL ANTHROPOLOGY
(2023)