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

Immunosenescence: molecular mechanisms and diseases DOI Creative Commons

Zaoqu Liu,

Qimeng Liang,

Yuqing Ren

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: May 13, 2023

Abstract Infection susceptibility, poor vaccination efficacy, age-related disease onset, and neoplasms are linked to innate adaptive immune dysfunction that accompanies aging (known as immunosenescence). During aging, organisms tend develop a characteristic inflammatory state expresses high levels of pro-inflammatory markers, termed inflammaging. This chronic inflammation is typical phenomenon immunosenescence it considered the major risk factor for diseases. Thymic involution, naïve/memory cell ratio imbalance, dysregulated metabolism, epigenetic alterations striking features immunosenescence. Disturbed T-cell pools antigen stimulation mediate premature senescence cells, senescent cells proinflammatory senescence-associated secretory phenotype exacerbates Although underlying molecular mechanisms remain be addressed, well documented T inflammaging might driving forces in Potential counteractive measures will discussed, including intervention cellular metabolic-epigenetic axes mitigate In recent years, has attracted increasing attention its role tumor development. As result limited participation elderly patients, impact on cancer immunotherapy unclear. Despite some surprising results from clinical trials drugs, necessary investigate other

Language: Английский

Citations

337
DNA damage and repair in age-related inflammation DOI
Yang Zhao, Matthew Simon, Andrei Seluanov

et al.

Nature reviews. Immunology, Journal Year: 2022, Volume and Issue: 23(2), P. 75 - 89

Published: July 13, 2022

Language: Английский

Citations

194
Chronic inflammation and the hallmarks of aging DOI Creative Commons
Jordan J. Baechle, Nan Chen, Priya Makhijani

et al.

Molecular Metabolism, Journal Year: 2023, Volume and Issue: 74, P. 101755 - 101755

Published: June 16, 2023

Recently, the hallmarks of aging were updated to include dysbiosis, disabled macroautophagy, and chronic inflammation. In particular, low-grade inflammation during aging, without overt infection, is defined as "inflammaging," which associated with increased morbidity mortality in population. Emerging evidence suggests a bidirectional cyclical relationship between development age-related conditions, such cardiovascular diseases, neurodegeneration, cancer, frailty. How crosstalk other underlies biological mechanisms disease thus particular interest current geroscience research.

Language: Английский

Citations

156
Epigenetic clock: A promising biomarker and practical tool in aging DOI
Ran Duan,

Qiaoyu Fu,

Yu Sun

et al.

Ageing Research Reviews, Journal Year: 2022, Volume and Issue: 81, P. 101743 - 101743

Published: Oct. 4, 2022

Language: Английский

Citations

150
Aging of mesenchymal stem cell: machinery, markers, and strategies of fighting DOI Creative Commons
Mahmoud Al‐Azab,

Mohammed Safi,

Elina Idiiatullina

et al.

Cellular & Molecular Biology Letters, Journal Year: 2022, Volume and Issue: 27(1)

Published: Aug. 19, 2022

Human mesenchymal stem cells (MSCs) are primary multipotent capable of differentiating into osteocytes, chondrocytes, and adipocytes when stimulated under appropriate conditions. The role MSCs in tissue homeostasis, aging-related diseases, cellular therapy is clinically suggested. As aging a universal problem that has large socioeconomic effects, an improved understanding the concepts can direct public policies reduce its adverse impacts on healthcare system humanity. Several studies have been carried out over several years to understand phenomenon different factors affecting human aging. A reduced ability adult cell populations reproduce regenerate one main contributors process. In this context, senescence major challenge front advancement. Many factors, ranging from genetic metabolic pathways extrinsic through various signaling pathways, involved regulating mechanism MSC senescence. To better reverse senescence, review highlights underlying mechanisms signs discusses strategies combat

Language: Английский

Citations

97
Mitochondrial-to-nuclear communication in aging: an epigenetic perspective DOI
Di Zhu, Xinyu Li, Ye Tian

et al.

Trends in Biochemical Sciences, Journal Year: 2022, Volume and Issue: 47(8), P. 645 - 659

Published: April 6, 2022

Language: Английский

Citations

92
Epigenetics, DNA damage, and aging DOI Creative Commons

Carolina Soto-Palma,

Laura J. Niedernhofer, Christopher Faulk

et al.

Journal of Clinical Investigation, Journal Year: 2022, Volume and Issue: 132(16)

Published: Aug. 14, 2022

Over the course of a human lifespan, genome integrity erodes, leading to an increased abundance several types chromatin changes. The DNA lesions (chemical perturbations nucleotides) increases with age, as does number genomic mutations and transcriptional disruptions caused by replication or transcription those lesions, respectively. At epigenetic level, precise methylation patterns degrade, likely causing increasingly stochastic variations in gene expression. Similarly, tight regulation histone modifications begins unravel. instability these mechanisms allows transposon element reactivation remobilization, further mutations, dysregulation, cytoplasmic fragments. This cumulative promotes cell signaling events that drive fate decisions extracellular communications known disrupt tissue homeostasis regeneration. In this Review, we focus on age-related changes their interactions instigate events.

Language: Английский

Citations

85
Fracture Healing in the Setting of Endocrine Diseases, Aging, and Cellular Senescence DOI Open Access
Dominik Saul, Sundeep Khosla

Endocrine Reviews, Journal Year: 2022, Volume and Issue: 43(6), P. 984 - 1002

Published: Feb. 19, 2022

Abstract More than 2.1 million age-related fractures occur in the United States annually, resulting an immense socioeconomic burden. Importantly, deterioration of bone structure is associated with impaired healing. Fracture healing a dynamic process which can be divided into four stages. While initial hematoma generates inflammatory environment mesenchymal stem cells and macrophages orchestrate framework for repair, angiogenesis cartilage formation mark second period. In central region, endochondral ossification favors soft callus development while next to fractured bony ends, intramembranous directly forms woven bone. The third stage characterized by removal calcification cartilage. Finally, chronic remodeling phase concludes process. Impaired fracture due aging related detrimental changes at cellular level. Macrophages, osteocytes, chondrocytes express markers senescence, leading reduced self-renewal proliferative capacity. A prolonged “inflammaging” results extended phase, senescent microenvironment deteriorating Although there evidence that setting injury, least some tissues, may play beneficial role facilitating tissue recent data demonstrate clearing enhances repair. this review, we summarize physiological as well pathological processes during endocrine disease order establish broad understanding biomechanical molecular mechanisms involved

Language: Английский

Citations

83
Cellular rejuvenation: molecular mechanisms and potential therapeutic interventions for diseases DOI Creative Commons

Shuaifei Ji,

Mingchen Xiong,

Huating Chen

et al.

Signal Transduction and Targeted Therapy, Journal Year: 2023, Volume and Issue: 8(1)

Published: March 14, 2023

Abstract The ageing process is a systemic decline from cellular dysfunction to organ degeneration, with more predisposition deteriorated disorders. Rejuvenation refers giving aged cells or organisms youthful characteristics through various techniques, such as reprogramming and epigenetic regulation. great leaps in rejuvenation prove that not one-way street, many rejuvenative interventions have emerged delay even reverse the process. Defining mechanism by which roadblocks signaling inputs influence complex programs essential for understanding developing strategies. Here, we discuss intrinsic extrinsic factors counteract cell rejuvenation, targeted core mechanisms involved this Then, critically summarize latest advances state-of-art strategies of rejuvenation. Various methods also provide insights treating specific ageing-related diseases, including reprogramming, removal senescence (SCs) suppression senescence-associated secretory phenotype (SASP), metabolic manipulation, stem cells-associated therapy, dietary restriction, immune heterochronic transplantation, etc. potential applications therapy extend cancer treatment. Finally, analyze detail therapeutic opportunities challenges technology. Deciphering will further into anti-ageing disease treatment clinical settings.

Language: Английский

Citations

82
Stress, diet, exercise: Common environmental factors and their impact on epigenetic age DOI Creative Commons
Fedor Galkin, Olga Kovalchuk, Diana Koldasbayeva

et al.

Ageing Research Reviews, Journal Year: 2023, Volume and Issue: 88, P. 101956 - 101956

Published: May 20, 2023

Epigenetic aging clocks have gained significant attention as a tool for predicting age-related health conditions in clinical and research settings. They enabled geroscientists to study the underlying mechanisms of assess effectiveness anti-aging therapies, including diet, exercise environmental exposures. This review explores effects modifiable lifestyle factors' on global DNA methylation landscape, seen by clocks. We also discuss through which these factors contribute biological provide comments what findings mean people willing build an evidence-based pro-longevity lifestyle.

Language: Английский

Citations

55