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Sivalingam AM. Emerging Mechanisms and Biomarkers Associated with T-Cells and B-Cells in Autoimmune Disorders. Clin Rev Allergy Immunol 2025; 68:14. [PMID: 39932617 DOI: 10.1007/s12016-025-09022-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/07/2025] [Indexed: 05/08/2025]
Abstract
Autoimmune diseases are characterized by the dysregulation of B-cells, which are responsible for antibody production against pathogens, and T-cells, which play a crucial role in cell-mediated immunity, including both helper and cytotoxic T-cells. These disorders frequently present with abnormal responses from both B- and T-cells, which can have a significant impact on cardiovascular health, particularly among the female patients. Key mechanisms contributing to these diseases include the activation of the NLRP3 inflammasome impaired efferocytosis is the process by which phagocytes clear apoptotic cells to maintain immune and developmental balance. Defects in this process can lead to inflammatory and autoimmune disorders. The gut microbiota helps defend against pathogens and signals immune cells, playing a vital role in human health and is involved in many aspects of the body. Novel therapeutic strategies such as nanomedicine and targeted treatments are being developed to restore immune balance. The significance of thymic homeostasis the influence of viral infections and the presence of tertiary lymphoid structures highlight the need for multidisciplinary approaches in the management of these conditions. A case study of a 9-year-old girl diagnosed with seronegative autoimmune encephalitis, who displayed severe obsessive-compulsive disorder (OCD) and aggressive behavior, exemplifies the complexities involved in treatment. Promising interventions, including CAR-T-cell therapy and nanomedicine, are under development for various autoimmune diseases, such as vitiligo and refractory autoimmune rheumatic diseases (ARDs). Furthermore, emerging therapies, including CAR-T-cell therapy, mRNA-based strategies, and microbiome modulation, are being explored alongside advancements in personalized medicine and early diagnostic techniques to improve patient outcomes for individuals affected by autoimmune diseases.
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Affiliation(s)
- Azhagu Madhavan Sivalingam
- Natural Products & Nanobiotechnology Research Lab, Department of Community Medicine, Saveetha Medical College and Hospital, Saveetha Institute of Medical and Technical Sciences (SIMATS), Saveetha University, Thandalam, Chennai, 602 105, Tamil Nadu, India.
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Cheng X, Yang J, Wang Z, Zhou K, An X, Xu ZZ, Lu H. Modulating intestinal viruses: A potential avenue for improving metabolic diseases with unresolved challenges. Life Sci 2025; 361:123309. [PMID: 39674267 DOI: 10.1016/j.lfs.2024.123309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2024] [Revised: 11/29/2024] [Accepted: 12/11/2024] [Indexed: 12/16/2024]
Abstract
The gut microbiome affects the occurrence and development of metabolic diseases, with a significant amount of research focused on intestinal bacteria. As an important part of the gut microbiome, gut viruses were studied recently, particularly through fecal virome transplantation (FVT), revealing manipulating the gut virus could reverse overweight and glucose intolerance in mice. And human cohort studies found gut virome changed significantly in patients with metabolic disease. By summarizing those studies, we compared the research and analytical methods, as well as the similarities and differences in their results, and analyzed the reasons for these discrepancies. FVT provided potential value to improve metabolic diseases, but the mechanisms involved and the effect of FVT on humans should be investigated further. The potential methods of regulating intestinal virome composition and the possible mechanisms of intestinal virome changes affecting metabolic diseases were also discussed.
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Affiliation(s)
- Xiaoxiao Cheng
- Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, PR China
| | - Jie Yang
- Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, PR China
| | - Zhijie Wang
- Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, PR China
| | - Kefan Zhou
- Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, PR China
| | - Xuejiao An
- Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, PR China
| | - Zhenjiang Zech Xu
- State Key Laboratory of Food Science and Technology, Nanchang University, Nanchang, PR China
| | - Hui Lu
- Jiangxi Agricultural University, College of Bioscience and Bioengineering, Nanchang, PR China.
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Vitek NS, Saks E, Dong A, Burroughs RW, Ward DL, Pomeroy E, Martin-Gronert M, Ozanne SE. Developmentally cascading structures do not lose evolutionary potential, but compound developmental instability in rat molars. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.13.632740. [PMID: 39868330 PMCID: PMC11761367 DOI: 10.1101/2025.01.13.632740] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Increasing variability down serially segmented structures, such as mammalian molar teeth and vertebrate limb segments, is a much-replicated pattern. The same phenotypic pattern has conflicting interpretations at different evolutionary scales. Macroevolutionary patterns are thought to reflect greater evolutionary potential in later-forming segments, but microevolutionary patterns are thought to reflect less evolutionary potential and greater phenotypic plasticity. We address this conflict by recalculating evolutionary potential (evolvability) from published mammalian molar data and directly measuring phenotypic plasticity from a controlled feeding experiment. Effects on lengths and widths are discordant in a way that suggests general growth pathways have a role in phenotypically plastic dental responses to nutrition. Effects on successive trait means do not necessarily increase downstream, contrary to long-standing hypotheses. We confirm prior findings of increasing non-inherited variance downstream, showing decoupling between effects on trait mean and variance. These patterns can be explained by a cascading model of tooth development compounding the effect of anatomically hyper-local developmental instability as an influence separate from general environmental effects on the developing embryo. When evaluated in terms of evolvability, not heritability, later-developing molars are equally or more evolvable than earlier-developing molars, aligning their microevolutionary potential with macroevolutionary patterns in other serially segmented structures.
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Affiliation(s)
- Natasha S Vitek
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, NY
| | - Ella Saks
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, NY
| | - Amy Dong
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, NY
| | - Robert W Burroughs
- Department of Ecology & Evolution, Stony Brook University, Stony Brook, NY
| | - Devin L Ward
- Department of Anthropology, University of Toronto, Toronto, Canada
| | - Emma Pomeroy
- Department of Archaeology and Newnham College, University of Cambridge, Cambridge, UK
| | - Malgorzata Martin-Gronert
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
| | - Susan E Ozanne
- Metabolic Research Laboratories and MRC Metabolic Diseases Unit, Institute of Metabolic Science, University of Cambridge, Cambridge, UK
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Burroughs RW, Percival CJ, Vitek NS. Reduced Dietary Protein Induces Changes in the Dental Proteome. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2025:2025.01.13.632248. [PMID: 39868298 PMCID: PMC11761009 DOI: 10.1101/2025.01.13.632248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/28/2025]
Abstract
Experimental studies have demonstrated that nutritional changes during development can result in phenotypic changes to mammalian cheek teeth. This developmental plasticity of tooth morphology is an example of phenotypic plasticity. Because tooth development occurs through complex interactions between manifold processes, there are many potential mechanisms which can contribute to a tooth's norm of reaction. Determining the identity of those mechanisms and the relative importance of each of them is one of the main challenges to understanding phenotypic plasticity. Quantitative proteomics combined with experimental studies allow for the identification of potential molecular contributors to a plastic response through quantification of expressed gene products. Here, we present the results of a quantitative proteomics analysis of mature upper first molars (M1s) in Mus musculus from a controlled feeding experiment. Pregnant and nursing mothers were fed either a low-dietary protein (10%) treatment diet or control (20%) diet. Expression of tooth-related proteins, immune system proteins, and actin-based myosin proteins were significantly altered in our low-dietary protein sample. The recovery of expression change in tooth development proteins was anticipated and consistent with previous proteomic studies. We also identified differential immune protein response along with systematic reduction in actin-based myosin protein expression, which are novel discoveries for tooth proteomics studies. We propose that studies which aim to elucidate specific mechanisms of molar phenotypic plasticity should prioritize investigations into the relationships between IGF regulation and tooth development and actin-based myosin expression and tooth development. Research Highlights A low-protein diet during development results in significantly altered protein expression for major dental building proteins, immune system proteins, and actin-based myosin proteins within Mus musculus .
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Liu JY, Yin X, Dong YT. Exploration of the shared gene signatures and molecular mechanisms between Alzheimer's disease and intracranial aneurysm. Sci Rep 2024; 14:24628. [PMID: 39427050 PMCID: PMC11490550 DOI: 10.1038/s41598-024-75694-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2024] [Accepted: 10/08/2024] [Indexed: 10/21/2024] Open
Abstract
Although Alzheimer's disease (AD) and intracranial aneurysm (IA) were two different types of diseases that occurred in the brain, ruptured IA (RIA) survivors may experience varying degrees of cognitive dysfunction. Neither AD nor IA is easily recognizable by an early onset so that the incidence of adverse clinical outcomes would be on the rise. Therefore, we focused on the exploration of the shared genes and molecular mechanisms between AD and IA, which would be significant for the efficiency of co-screening and co-diagnosis. Two GEO datasets were selected for the weighted gene co-expression network analysis (WGCNA) and differentially expressed gene screening, obtaining 78 overlapped genes. Next, 9 hub genes were identified by the protein-protein interaction network, including PIK3CA, GAB1, IGF1R, PLCB1, PGR, PDGFRB, PLCE1, FGFR3, and SYNJ1. The interactions among the hub genes, miRNA, and TFs were also explored. Meanwhile, we performed GO and KEGG pathway enrichment analyses for the results of WGCNA and hub genes, which showed that the Ras signaling and Rap1 signaling were the main shared pathogenesis. In conclusion, the present bioinformatics analysis revealed that AD and IA had the shared genes and molecular mechanisms, and these outcomes were associated with inflammation and calcium homeostasis, which could provide research clues for further studies.
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Affiliation(s)
- Ji-Yun Liu
- Department of Clinical Laboratory, Guiyang Second People's Hospital, Guiyang, People's Republic of China
| | - Xuan Yin
- Department of Women Healthcare, Guiyang Maternal and Child Health Hospital, Guiyang, People's Republic of China
| | - Yang-Ting Dong
- Key Laboratory of Endemic and Ethnic Diseases (Guizhou Medical University) of the Ministry of Education and Provincial Key Laboratory of Medical Molecular Biology, No. 9, Beijing Road, Guiyang, 550004, People's Republic of China.
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Ali A, Zhang Z, Gao T, Aleksic S, Gavathiotis E, Barzilai N, Milman S. Identification of functional rare coding variants in IGF-1 gene in humans with exceptional longevity. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.10.11.617885. [PMID: 39416202 PMCID: PMC11482895 DOI: 10.1101/2024.10.11.617885] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 10/19/2024]
Abstract
Diminished signaling via insulin/insulin-like growth factor-1 (IGF-1) axis is associated with longevity in different model organisms. IGF-1 gene is highly conserved across species, with only few evolutionary changes identified in it. Despite its potential role in regulating lifespan, no coding variants in IGF-1 have been reported in human longevity cohorts to date. This study investigated the whole exome sequencing data from 2,487 individuals in a cohort of Ashkenazi Jewish centenarians, their offspring, and controls without familial longevity to identify functional IGF-1 coding variants. We identified two likely functional coding variants IGF-1:p.Ile91Leu and IGF-1:p.Ala118Thr in our longevity cohort. Notably, a centenarian specific novel variant IGF-1:p.Ile91Leu was located at the binding interface of IGF-1 - IGF-1R, whereas IGF-1:p.Ala118Thr was significantly associated with lower circulating levels of IGF-1. We performed extended all-atom molecular dynamics simulations to evaluate the impact of Ile91Leu on stability, binding dynamics and energetics of IGF-1 bound to IGF-1R. The IGF-1:p.Ile91Leu formed less stable interactions with IGF-1R's critical binding pocket residues and demonstrated lower binding affinity at the extracellular binding site compared to wild-type IGF-1. Our findings suggest that IGF-1:p.Ile91Leu and IGF-1:p.Ala118Thr variants attenuate IGF-1R activity by impairing IGF-1 binding and diminishing the circulatory levels of IGF-1, respectively. Consequently, diminished IGF-1 signaling resulting from these variants may contribute to exceptional longevity in humans.
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Affiliation(s)
- Amanat Ali
- Department of Medicine, Albert Einstein College of Medicine, NY, USA, 10461
- Institute for Aging Research and the Einstein-NSC, Albert Einstein College of Medicine, NY, USA, 10461
| | - Zhengdong Zhang
- Department of Genetics, Albert Einstein College of Medicine, NY, USA, 10461
- Institute for Aging Research and the Einstein-NSC, Albert Einstein College of Medicine, NY, USA, 10461
| | - Tina Gao
- Department of Medicine, Albert Einstein College of Medicine, NY, USA, 10461
- Institute for Aging Research and the Einstein-NSC, Albert Einstein College of Medicine, NY, USA, 10461
| | - Sandra Aleksic
- Department of Medicine, Albert Einstein College of Medicine, NY, USA, 10461
- Institute for Aging Research and the Einstein-NSC, Albert Einstein College of Medicine, NY, USA, 10461
| | - Evripidis Gavathiotis
- Department of Medicine, Albert Einstein College of Medicine, NY, USA, 10461
- Department of Biochemistry, Albert Einstein College of Medicine, NY, USA, 10461
- Institute for Aging Research and the Einstein-NSC, Albert Einstein College of Medicine, NY, USA, 10461
| | - Nir Barzilai
- Department of Medicine, Albert Einstein College of Medicine, NY, USA, 10461
- Department of Genetics, Albert Einstein College of Medicine, NY, USA, 10461
- Institute for Aging Research and the Einstein-NSC, Albert Einstein College of Medicine, NY, USA, 10461
| | - Sofiya Milman
- Department of Medicine, Albert Einstein College of Medicine, NY, USA, 10461
- Department of Genetics, Albert Einstein College of Medicine, NY, USA, 10461
- Institute for Aging Research and the Einstein-NSC, Albert Einstein College of Medicine, NY, USA, 10461
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