GeneSetCart: assembling, augmenting, combining, visualizing, and analyzing gene sets DOI Creative Commons
Giacomo B. Marino, Stephanie Olaiya, John Erol Evangelista

et al.

GigaScience, Journal Year: 2025, Volume and Issue: 14

Published: Jan. 1, 2025

Abstract Converting multiomics datasets into gene sets facilitates data integration that leads to knowledge discovery. Although there are tools developed analyze sets, only a few offer the management of from multiple sources. GeneSetCart is an interactive web-based platform enables investigators gather various sources; augment these with gene–gene coexpression correlations and protein–protein interactions; perform set operations on such as union, consensus, intersection; visualize all in one place. supports upload single or well fetching by searching PubMed for genes comentioned terms publications. Venn diagrams, heatmaps, Uniform Manifold Approximation Projection (UMAP) plots, SuperVenn UpSet plots can session summarize similarity overlap among sets. Users also enrichment analysis their assembled external tools. All be saved user account reanalysis sharing collaborators. has library crossing feature created several National Institutes Health Common Fund programs. For top overlapping pairs programs, large language model (LLM) prompted propose possible reasons high overlap. Using this feature, two use cases presented. In addition, users produce publication-ready reports uploaded Text supplemented LLM. Overall, useful resource enabling biologists without programming expertise facilitate hypothesis generation.

Language: Английский

Genomic Instability and Epigenetic Changes during Aging DOI Open Access

Lucía López-Gil,

Amparo Pascual‐Ahuir, Markus Proft

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(18), P. 14279 - 14279

Published: Sept. 19, 2023

Aging is considered the deterioration of physiological functions along with an increased mortality rate. This scientific review focuses on central importance genomic instability during aging process, encompassing a range cellular and molecular changes that occur advancing age. In particular, this revision addresses genetic epigenetic alterations contribute to instability, such as telomere shortening, DNA damage accumulation, decreased repair capacity. Furthermore, explores aging, including modifications histones, methylation patterns, role non-coding RNAs. Finally, discusses organization chromatin its contribution heterochromatin loss, remodeling, in nucleosome histone abundance. conclusion, highlights fundamental plays process underscores need for continued research into these complex biological mechanisms.

Language: Английский

Citations

47
Aberrant chromatin reorganization in cells from diseased fibrous connective tissue in response to altered chemomechanical cues DOI
Su‐Jin Heo,

Shreyasi Thakur,

Xingyu Chen

et al.

Nature Biomedical Engineering, Journal Year: 2022, Volume and Issue: 7(2), P. 177 - 191

Published: Aug. 22, 2022

Language: Английский

Citations

49
Aging conundrum: A perspective for ovarian aging DOI Creative Commons
Jiachen Wu,

Yang Liu,

Yinhua Song

et al.

Frontiers in Endocrinology, Journal Year: 2022, Volume and Issue: 13

Published: Aug. 19, 2022

Progressive loss of physiological integrity and accumulation degenerative changes leading to functional impairment increased susceptibility diseases are the main features aging. The ovary, key organ that maintains female reproductive endocrine function, enters aging earlier faster than other organs has attracted extensive attention from society. Ovarian is mainly characterized by progressive decline in number quality oocytes, regulatory mechanisms which have yet be systematically elucidated. This review discusses hallmarks further highlight characteristics ovarian attempt explore its clinical symptoms underlying mechanisms. Finally, intervention strategies related elaborated, especially potential role stem cells cryopreservation embryos, or tissue delay

Language: Английский

Citations

43
Epigenetic Mechanisms of Aging and Aging-Associated Diseases DOI Creative Commons
Annamaria la Torre, Filomena Lo Vecchio, Antonio Greco

et al.

Cells, Journal Year: 2023, Volume and Issue: 12(8), P. 1163 - 1163

Published: April 14, 2023

Aging is an inevitable outcome of life, characterized by a progressive decline in tissue and organ function. At molecular level, it marked the gradual alterations biomolecules. Indeed, important changes are observed on DNA, as well at protein that influenced both genetic environmental parameters. These directly contribute to development or progression several human pathologies, including cancer, diabetes, osteoporosis, neurodegenerative disorders others aging-related diseases. Additionally, they increase risk mortality. Therefore, deciphering hallmarks aging represents possibility for identifying potential druggable targets attenuate process, then age-related comorbidities. Given link between aging, genetic, epigenetic alterations, given reversible nature mechanisms, precisely understanding these factors may provide therapeutic approach disease. In this review, we center regulatory mechanisms their aging-associated changes, highlighting inferences age-associated

Language: Английский

Citations

42
Aging microenvironment and antitumor immunity for geriatric oncology: the landscape and future implications DOI Creative Commons
Binghao Zhao, Bo Wu, Nan Feng

et al.

Journal of Hematology & Oncology, Journal Year: 2023, Volume and Issue: 16(1)

Published: March 21, 2023

The tumor microenvironment (TME) has been extensively investigated; however, it is complex and remains unclear, especially in elderly patients. Senescence a cellular response to variety of stress signals, which characterized by stable arrest the cell cycle major changes morphology physiology. To best our knowledge, senescence leads consistent cells remodeling tumor-immune (TIME) activating set pleiotropic cytokines, chemokines, growth factors, proteinases, constitute senescence-associated secretory phenotype (SASP). On one hand, SASP promotes antitumor immunity, enhances treatment efficacy; on other increases immunosuppressive infiltration, including myeloid-derived suppressor (MDSCs), regulatory T (Tregs), M2 macrophages, N2 neutrophils, contributing TIME suppression. Therefore, deeper understanding regulation components robust immunity individuals with different cancer types available therapies necessary control provide greater clinical benefits In this review, we summarize key biological functions mediated cytokines intercellular interactions significant TME landscape, influence immunotherapy geriatric oncology. Furthermore, recent advances practices targeting discuss potential senescent targets.

Language: Английский

Citations

27
Deciphering the role of immune cell composition in epigenetic age acceleration: Insights from cell‐type deconvolution applied to human blood epigenetic clocks DOI Creative Commons
Ze Zhang, Samuel R. Reynolds, Hannah Stolrow

et al.

Aging Cell, Journal Year: 2023, Volume and Issue: 23(3)

Published: Dec. 25, 2023

Abstract Aging is a significant risk factor for various human disorders, and DNA methylation clocks have emerged as powerful tools estimating biological age predicting health‐related outcomes. Methylation data from blood has been focus of more recently developed clocks. However, the impact immune cell composition on epigenetic acceleration (EAA) remains unclear only some incorporate partial type information when analyzing EAA. We investigated associations 12 types measured by cell‐type deconvolution with EAA predicted six widely‐used in >10,000 samples. observed all tested. Across clocks, nine or tested exhibited Higher memory lymphocyte subtype proportions were associated increased EAA, naïve subtypes decreased To demonstrate potential confounding composition, we applied rheumatoid arthritis. Our research maps contributions to offers opportunities adjust studies significantly granular level. Understanding profiles implications interpretation its relevance aging disease research. detailed map serves resource utilizing across diverse fields, including aging‐related diseases, precision medicine, therapeutic interventions.

Language: Английский

Citations

26
Post‐translational regulation of muscle growth, muscle aging and sarcopenia DOI Creative Commons
Qian Zhong, Kun Zheng, Wanmeng Li

et al.

Journal of Cachexia Sarcopenia and Muscle, Journal Year: 2023, Volume and Issue: 14(3), P. 1212 - 1227

Published: May 1, 2023

Abstract Skeletal muscle makes up 30–40% of the total body mass. It is great significance in maintaining digestion, inhaling and exhaling, sustaining posture, exercising, protecting joints many other aspects. Moreover, also an important metabolic organ that helps to maintain balance sugar fat. Defective skeletal function not only limits daily activities elderly but increases risk disability, hospitalization death, placing a huge burden on society healthcare system. Sarcopenia progressive decline mass, strength with age caused by environmental genetic factors, such as abnormal regulation protein post‐translational modifications (PTMs). To date, studies have shown numerous PTMs, phosphorylation, acetylation, ubiquitination, SUMOylation, glycosylation, glycation, methylation, S‐nitrosylation, carbonylation S‐glutathionylation, are involved health diseases. This article systematically summarizes growth atrophy understand pathophysiology aging develop effective strategies for diagnosing, preventing treating sarcopenia.

Language: Английский

Citations

25
Vitamin D Improves Cognitive Impairment and Alleviates Ferroptosis via the Nrf2 Signaling Pathway in Aging Mice DOI Open Access
Jiaxin Li, Yang Cao, Jie Xu

et al.

International Journal of Molecular Sciences, Journal Year: 2023, Volume and Issue: 24(20), P. 15315 - 15315

Published: Oct. 18, 2023

Ferroptosis is an iron-dependent mode of cell death associated with the occurrence and development age-related neurodegenerative diseases. Currently, there are no effective drugs available to prevent or treat these aging-related Vitamin D (VD) antioxidant immunomodulator, but its relationship ferroptosis in diseases has not been extensively studied. In this study, we aimed investigate role VD learning memory aging mice. To examine whether protects hippocampal neurons, used physiologically active 1,25(OH)2D3. We established models vivo (C57BL/6 mice) vitro (HT22 cells) using D-galactose (D-gal). The results demonstrated that could improve mice aged via use D-gal, it reduced damage neurons. regulate ferroptosis-related proteins (increasing GPX4 expression decreasing ACSL4 ALOX15 protein levels), increasing GSH levels, reducing MDA intracellular mitochondrial ROS as well total iron Fe2+ improving morphology, thereby alleviating Additionally, activated VDR/Nrf2/HO-1 signaling pathway, inhibiting ferroptosis. Notably, when VDR was knocked down, lost ability activate Nrf2. Consequently, Nrf2 decreased protective effect against summary, activates Nrf2/HO-1 pathway through VDR, effectively preventing induced by

Language: Английский

Citations

23
Emerging roles of mitochondrial functions and epigenetic changes in the modulation of stem cell fate DOI Open Access
Chen‐Song Zhang, Yang Meng, Junhong Han

et al.

Cellular and Molecular Life Sciences, Journal Year: 2024, Volume and Issue: 81(1)

Published: Jan. 12, 2024

Language: Английский

Citations

15
Replication stress as a driver of cellular senescence and aging DOI Creative Commons
Lauren M. Herr, Ethan Schaffer,

Kathleen F. Fuchs

et al.

Communications Biology, Journal Year: 2024, Volume and Issue: 7(1)

Published: May 22, 2024

Abstract Replication stress refers to slowing or stalling of replication fork progression during DNA synthesis that disrupts faithful copying the genome. While long considered a nexus for damage, role in aging is under-appreciated. The consequential promotion organismal phenotypes evidenced by an extensive list hereditary accelerated disorders marked molecular defects factors promote and operate uniquely response. Additionally, recent studies have revealed cellular pathways elicited align with designated hallmarks aging. Here we review advances demonstrating as ultimate driver senescence We discuss clinical implications intriguing links between including application senotherapeutic approaches context stress.

Language: Английский

Citations

15